diff --git a/src/application/EvidenceBundleCommands.ts b/src/application/EvidenceBundleCommands.ts
index 0da3db244f..3205f867ca 100644
--- a/src/application/EvidenceBundleCommands.ts
+++ b/src/application/EvidenceBundleCommands.ts
@@ -4,7 +4,6 @@ import { requireAuthenticationHeadroom } from "./JsonAuthenticationHeadroom.js";
 
 import {
   EvidenceFileError,
-  EvidenceIntegrityError,
   type PublishedEvidenceFile,
 } from "../domain/evidenceErrors.js";
 import type { AnalysisError } from "../domain/analysisErrorBase.js";
@@ -256,15 +255,7 @@ export const compareEvidenceBundlesCommand = async (input: {
   ]);
   if (!left.ok) return left;
   if (!right.ok) return right;
-  try {
-    return ok(jsonValueSchema.parse(compareBundles(left.value, right.value)));
-  } catch (cause: unknown) {
-    return err(
-      new EvidenceIntegrityError("Evidence bundle comparison failed", {
-        cause,
-      }),
-    );
-  }
+  return ok(jsonValueSchema.parse(compareBundles(left.value, right.value)));
 };
 
 const projectWrite = (
diff --git a/src/domain/bundleComparison.test.ts b/src/domain/bundleComparison.test.ts
index 866c09be23..f91aff856e 100644
--- a/src/domain/bundleComparison.test.ts
+++ b/src/domain/bundleComparison.test.ts
@@ -5,6 +5,7 @@ import {
   bundleComparisonResultSchema,
   compareBundles,
 } from "./bundleComparison.js";
+import { AnalysisInputError } from "./analysisErrorCore.js";
 import { createEvidence } from "./evidence.js";
 import { createEvidenceBundle } from "./evidenceBundle.js";
 import {
@@ -202,7 +203,7 @@ describe("bundle comparison", () => {
           right_evidence_id: rightRecord.evidence_id,
         },
       ]),
-    ).toThrow(/missing left evidence/u);
+    ).toThrow(AnalysisInputError);
     expect(() =>
       compareBundles(left, right, [
         {
@@ -214,7 +215,7 @@ describe("bundle comparison", () => {
           right_evidence_id: rightRecord.evidence_id,
         },
       ]),
-    ).toThrow(/one-to-one/u);
+    ).toThrow(AnalysisInputError);
     expect(() =>
       compareBundles({ ...left, records: [leftRecord, leftRecord] }, right),
     ).toThrow(/duplicate record IDs/u);
diff --git a/src/domain/bundleComparison.ts b/src/domain/bundleComparison.ts
index 6e918e22f5..f2b5dd9905 100644
--- a/src/domain/bundleComparison.ts
+++ b/src/domain/bundleComparison.ts
@@ -7,6 +7,7 @@ import {
   serializeEvidenceBundle,
   type EvidenceBundle,
 } from "./evidenceBundle.js";
+import { AnalysisInputError } from "./analysisErrorCore.js";
 import type { ResidualUnknown } from "./residualUnknown.js";
 import { digestSchema } from "./../domain/digests.js";
 import { prefixedDigestSchema } from "./../domain/digests.js";
@@ -130,20 +131,31 @@ const compareRecords = (
   const pairedRight = new Set<string>();
   const changes: BundleChange[] = [];
   let changed = 0;
-  for (const pair of pairs) {
+  for (const [index, pair] of pairs.entries()) {
     if (!leftIds.has(pair.left_evidence_id))
-      throw new TypeError(
+      throw recordPairFailure(
+        index,
+        "left_evidence_id",
         `Explicit pair references missing left evidence ${pair.left_evidence_id}`,
       );
     if (!rightIds.has(pair.right_evidence_id))
-      throw new TypeError(
+      throw recordPairFailure(
+        index,
+        "right_evidence_id",
         `Explicit pair references missing right evidence ${pair.right_evidence_id}`,
       );
-    if (
-      pairedLeft.has(pair.left_evidence_id) ||
-      pairedRight.has(pair.right_evidence_id)
-    )
-      throw new TypeError("Explicit evidence pairs must be one-to-one");
+    if (pairedLeft.has(pair.left_evidence_id))
+      throw recordPairFailure(
+        index,
+        "left_evidence_id",
+        "Explicit evidence pairs must be one-to-one",
+      );
+    if (pairedRight.has(pair.right_evidence_id))
+      throw recordPairFailure(
+        index,
+        "right_evidence_id",
+        "Explicit evidence pairs must be one-to-one",
+      );
     pairedLeft.add(pair.left_evidence_id);
     pairedRight.add(pair.right_evidence_id);
     if (pair.left_evidence_id === pair.right_evidence_id) continue;
@@ -198,6 +210,15 @@ const compareRecords = (
   };
 };
 
+const recordPairFailure = (
+  index: number,
+  field: keyof RecordPair,
+  message: string,
+): AnalysisInputError =>
+  new AnalysisInputError("compare_bundles", { userMessage: message }, [
+    { path: ["record_pairs", index, field], reason: "invalid_value", message },
+  ]);
+
 const compareUnknowns = (left: EvidenceBundle, right: EvidenceBundle) => {
   const leftHistories = histories(left.unknowns);
   const rightHistories = histories(right.unknowns);
diff --git a/tests/boundary/mcp/bundleComparisonMcp.test.ts b/tests/boundary/mcp/bundleComparisonMcp.test.ts
index a5ae67f41d..cbe44655d5 100644
--- a/tests/boundary/mcp/bundleComparisonMcp.test.ts
+++ b/tests/boundary/mcp/bundleComparisonMcp.test.ts
@@ -367,6 +367,119 @@ describe("bundle comparison MCP integration", () => {
   });
 });
 
+describe("bundle comparison record selections", () => {
+  it.each([
+    {
+      label: "missing left evidence",
+      pairs: (
+        _left: readonly ReturnType<typeof sourceEvidence>[],
+        right: readonly ReturnType<typeof sourceEvidence>[],
+      ) => [
+        {
+          left_evidence_id: sourceEvidence("absent-left").evidence_id,
+          right_evidence_id: right[0]!.evidence_id,
+        },
+      ],
+      path: ["record_pairs", 0, "left_evidence_id"],
+      message: "missing left evidence",
+    },
+    {
+      label: "missing right evidence",
+      pairs: (
+        left: readonly ReturnType<typeof sourceEvidence>[],
+        _right: readonly ReturnType<typeof sourceEvidence>[],
+      ) => [
+        {
+          left_evidence_id: left[0]!.evidence_id,
+          right_evidence_id: sourceEvidence("absent-right").evidence_id,
+        },
+      ],
+      path: ["record_pairs", 0, "right_evidence_id"],
+      message: "missing right evidence",
+    },
+    {
+      label: "duplicate left evidence",
+      pairs: (
+        left: readonly ReturnType<typeof sourceEvidence>[],
+        right: readonly ReturnType<typeof sourceEvidence>[],
+      ) => [
+        {
+          left_evidence_id: left[0]!.evidence_id,
+          right_evidence_id: right[0]!.evidence_id,
+        },
+        {
+          left_evidence_id: left[0]!.evidence_id,
+          right_evidence_id: right[1]!.evidence_id,
+        },
+      ],
+      path: ["record_pairs", 1, "left_evidence_id"],
+      message: "one-to-one",
+    },
+    {
+      label: "duplicate right evidence",
+      pairs: (
+        left: readonly ReturnType<typeof sourceEvidence>[],
+        right: readonly ReturnType<typeof sourceEvidence>[],
+      ) => [
+        {
+          left_evidence_id: left[0]!.evidence_id,
+          right_evidence_id: right[0]!.evidence_id,
+        },
+        {
+          left_evidence_id: left[1]!.evidence_id,
+          right_evidence_id: right[0]!.evidence_id,
+        },
+      ],
+      path: ["record_pairs", 1, "right_evidence_id"],
+      message: "one-to-one",
+    },
+  ])(
+    "reports the precise path for $label without publishing Evidence",
+    async ({ pairs, path, message }) => {
+      const root = await createTestTempDirectory(
+        "rea-bundle-pairs-invalid-mcp-",
+      );
+      roots.push(root);
+      const left = [sourceEvidence("left-1"), sourceEvidence("left-2")];
+      const right = [sourceEvidence("right-1"), sourceEvidence("right-2")];
+      const leftPath = join(root, "left.json");
+      const rightPath = join(root, "right.json");
+      await Promise.all([
+        writeFile(
+          leftPath,
+          serializeEvidenceBundle(createEvidenceBundle(left)),
+        ),
+        writeFile(
+          rightPath,
+          serializeEvidenceBundle(createEvidenceBundle(right)),
+        ),
+      ]);
+      const connected = await connect();
+      try {
+        const result = await connected.client.callTool({
+          name: "compare_bundles",
+          arguments: {
+            left_bundle_path: leftPath,
+            right_bundle_path: rightPath,
+            record_pairs: pairs(left, right),
+          },
+        });
+        expect(parseMcpToolError(result).error).toMatchObject({
+          code: "invalid_request",
+          category: "invalid_input",
+          message: expect.stringContaining(message),
+          details: {
+            issues: [expect.objectContaining({ path })],
+          },
+        });
+        expect(connected.session.exportEvidenceBundle().records).toEqual([]);
+      } finally {
+        await connected.close();
+      }
+    },
+  );
+});
+
 const connect = async () => {
   const session = createTestBinarySession(() => ({
     health: () => Promise.resolve(),
@@ -381,6 +494,7 @@ const connect = async () => {
   await client.connect(clientTransport);
   return {
     client,
+    session,
     close: async () => {
       await Promise.allSettled([
         client.close(),
diff --git a/tests/process-global/bundleComparisonFailures.test.ts b/tests/process-global/bundleComparisonFailures.test.ts
new file mode 100644
index 0000000000..31e4d6cf19
--- /dev/null
+++ b/tests/process-global/bundleComparisonFailures.test.ts
@@ -0,0 +1,64 @@
+import { writeFile } from "node:fs/promises";
+import { join } from "node:path";
+
+import { expect, it, onTestFinished, vi } from "vitest";
+import { z } from "zod";
+
+import { createCli } from "../../src/cli.js";
+import { compareEvidenceBundlesCommand } from "../../src/application/EvidenceBundleCommands.js";
+import { bundleComparisonResultSchema } from "../../src/domain/bundleComparison.js";
+import {
+  createEvidenceBundle,
+  serializeEvidenceBundle,
+} from "../../src/domain/evidenceBundle.js";
+import { createTestTempDirectory } from "../fixtures/temporaryDirectory.js";
+
+it.each([
+  new TypeError("comparison output invariant failed"),
+  new RangeError("comparison computation failed"),
+  new z.ZodError([
+    { code: "custom", path: ["status"], message: "invalid generated result" },
+  ]),
+])(
+  "keeps an internal comparison failure distinct from damaged Evidence: $name",
+  async (failure) => {
+    const directory = await createTestTempDirectory(
+      "rea-bundle-compute-failure-",
+    );
+    const path = join(directory, "bundle.json");
+    await writeFile(path, serializeEvidenceBundle(createEvidenceBundle([])));
+    // Reach output validation through the actual command, reader, authentication
+    // and comparison. This fault is generated output, not the caller's bundle.
+    const output = vi
+      .spyOn(bundleComparisonResultSchema, "parse")
+      .mockImplementation(() => {
+        throw failure;
+      });
+    onTestFinished(() => output.mockRestore());
+
+    const originalExitCode = process.exitCode;
+    onTestFinished(() => {
+      process.exitCode = originalExitCode;
+    });
+    process.exitCode = 0;
+    let stdout = "";
+    let exitCode = 0;
+    await createCli({}).serve(["compare", path, path, "--json"], {
+      env: {},
+      stdout: (chunk) => {
+        stdout += chunk;
+      },
+      exit: (code) => {
+        exitCode = code;
+      },
+    });
+    expect(exitCode || Number(process.exitCode ?? 0)).toBe(1);
+    expect(JSON.parse(stdout)).toEqual({
+      code: "UNKNOWN",
+      message: failure.message,
+    });
+    await expect(
+      compareEvidenceBundlesCommand({ leftPath: path, rightPath: path }),
+    ).rejects.toBe(failure);
+  },
+);