It’s likely that you have a directory checked into revision control (the directory these problematic files are in). If you are in a new-ish project and don’t care about your git history (this is what i did).
- BACK UP YOUR GIT DIRECTORY
- git init
- add problematic dirs to .gitignore
- re-commit files
If you’d like to preserve your history I’m sure there is a way but i’m not sure what i’d do if i needed to preserve the repo but this thread looks to have promising solutions.