That is fine, just remove them!
Python auto-generates them from the corresponding .py file any time it wants to, so you needn't worry about simply deleting them all from your repository.
A couple of related tips - if you don't want them generated at all on your local dev machine, set the environment variable PYTHONDONTWRITEBYTECODE=1
. Python 3.2 fixed the annoyance of source folders cluttered with .pyc files with a new __pycache__
subfolder