I had the same issue. Using verbose helped me to find out a bit more the reason:
$ pip3 uninstall --verbose my-homemade-package
Not sure how to uninstall: my-homemade-package e48e635 - Check: /home/olivier/my-homemade-package
Can't uninstall 'my-homemade-package'. No files were found to uninstall.
Removing everything that was ‘my-homemade-package’ related in /usr/local/python2.x and /usr/local/python3.x did not help.
I did a pip3 show my-homemade-package and got the location of the installed package on my computer:
$ pip3 show my-homemade-package
Name: my-homemade-package
Version: e48e635
Summary: My Home Made package
Home-page: UNKNOWN
Author: UNKNOWN
Author-email: UNKNOWN
License: Proprietary
Location: /home/olivier/my-homemade-package
Requires: pyOpenSSL, pyasn1, protobuf
Removing /home/olivier/my-homemade-package sorted it out the issue (ie: the package was not listed).