I got the following issue during one of the scans:

Could not process some files due to syntax errors
View workflow run
A parse error occurred: Comments are not legal in JSON.. Check the syntax of the file. If the file is invalid, correct the error or exclude the file from analysis.

CodeQL also found 2 other warnings like this. See the workflow log for details.

The thing is, it's impossible to find the problematic files within the workflow log:
| Diagnostic | Summary |
+---------------------------------------------------+------------------------+
| Extraction errors | 13 results (13 errors) |
| Could not process some files due to syntax errors | 3 results (3 warnings) |
| Successfully extracted files | 548 results |

That's kinda it, I couldn't find the mentioned files there.