actions/stale paginates through issues and pull requests and makes an API call per action it takes. On a large backlog it can exhaust the hourly REST API limit for the token in a single run.
What this error means
A stale workflow fails partway through with "API rate limit exceeded", leaving some issues unprocessed.
github-actions
Error: API rate limit exceeded for installation ID xxxxx.
##[error]You have exceeded a secondary rate limit.
Common causes
Too many operations per run
A large backlog plus a high operations-per-run consumes the API budget quickly.
Secondary rate limits
Rapid write operations can trip secondary abuse limits even below the primary cap.
How to fix it
Throttle the stale run
Lower operations-per-run to spread work across scheduled runs.
Run the workflow more frequently with smaller batches.
Narrow the scope with labels or only-issues/only-PRs.