When calling one of those commands, vim-plug confuses all plugins URIs with the URI of the current folder.

For example, running PlugStatus when in ~/.vim (which contains its own git repository) results in this:

Finished. 74 error(s).
x vim-cute-python:
     Invalid URI: https://github.com/Xifax/yavir.git
     Expected:    https://git:@github.com/ehamberg/vim-cute-python.git
     PlugClean required.
     ...

PlugInstall and PlugUpdate work perfectly well.