[BUG] Routines: GitHub MCP search_issues returns total_count 0 for any free-text term in a private repo (qualifier-only queries work)

Summary

In a scheduled routine (Claude Code on the web), the built-in GitHub MCP tool mcp__github__search_issues returns {"total_count":0,"incomplete_results":false,"items":[]} whenever the query contains a free-text term, even though matching issues exist in the repository. Queries that use only qualifiers (e.g. is:open, label:...) return the correct results. No error is raised, so an agent reads "0 results" as "nothing matches".

The same queries return the expected results locally with gh api search/issues (personal OAuth token).

Environment

• Surface: Claude Code routines (scheduled cloud agent), environment "Default", model claude-sonnet-5
• Repository: a private repository owned by a personal account, added as a source of the routine (the Claude GitHub App has access; list_issues and issue_read work)
• Date observed: 2026-09-23

Steps to reproduce

Run a routine that calls search_issues sequentially (one call at a time) with owner/repo set to the private repository:

| query | routine (search_issues) | local (gh api search/issues, same repo) |
|---|---|---|
| is:open | 89 | 89 |
| is:open label:<label> | 4 | 4 |
| is:open conhost | 0 | 2 |
| is:open Opus | 0 | 3 |
| is:open Grok | 0 | 5 |
| is:open ConoHa | 0 | 9 |
| is:open Playwright | 0 | 6 |
| is:open Notion | 0 | 9 |
| repo:<owner>/<repo> is:issue is:open "2026-09-24" in:body | 0 | 3 |

Additional observations:

• An issue returned by the is:open query contained the word BlogBotInventory in its body, but searching for BlogBotInventory did not return that issue.
• Quoting, removing quotes, adding or removing in:body, and passing or omitting the owner/repo arguments made no difference.
• In one run where the calls were made in parallel, a few free-text queries returned 1 result instead of 0; with sequential calls, all free-text queries returned 0.

Expected

Free-text queries return the same matches as the REST search API does for the repository owner (as with gh).

Actual

Free-text queries return total_count: 0 without an error. Qualifier-only queries are correct.

Possibly related

• The official github-mcp-server calls GET /search/issues with is:issue repo:owner/repo prepended, which is the same request gh makes, so the difference seems to be the credential (Claude GitHub App vs. personal token).
• A similar symptom has been reported for code search with GitHub App tokens on private repositories: https://github.com/orgs/community/discussions/113651 (that report is about /search/code, so I have not confirmed that it is the same cause).

Impact / workaround

A routine that narrowed candidates with a date search silently missed issues. We switched to list_issues (fetching all open issues) and filtering locally, which works but is much heavier.