It seems there is a UI bug in Actions and Check Runs UIs. ❌ is not updated to 🟡 when a Re-Run button is hit even though other elements in the UI show that something is running.
See the attached screenshots.
This definitely does not look like the intended behavior. If this happens again, I suggest getting in contact with GitHub support but you could always push to the repo again to get past this.
Alternatively, the new GitHub Actions API may allow you to fix this in the future.