Have you faced a note on CRAN about non-standard things in the check directory ?
Check: for non-standard things in the check directory Result: NOTE Found the following files/directories: ‘extrapackage’
Maybe you do not understand where these files came from.
Then, you can run
check_clean_userspace() in your package
directory to detect every files that you created during the check.
They could be issued from examples, tests or vignettes:
check_clean_userspace() will tell you.