To reproduce:

1. Make sure CodeQL is in your path and the CodeQL repo is available
2. Run ./repro.sh

You can also play around with setting the OPT environment variable to see how the optimization level for some reason changes the behavior :(

$ OPT=-O0 ./repro.sh

Note: I also just tried this on a Mac and over there both files individually were missed but the two together were both flagged. Mysterious!