I started getting it in [#4205](https://github.com/geany/geany/pull/4205) and now it fails also for the merged [#4095](https://github.com/geany/geany/pull/4095) in master.
If you pushed to those branches multiple times, the subsequent builds used cached objects; CodeQL was not built to cope with those:
Since CodeQL observes the activity of the compiler to understand the data flows in a repository, CodeQL requires a complete build to take place in order to perform analysis.