I have been using Ubuntu 16.04 since more than a year. Recently I had to build a couple of softwares from source, due to dependency issues I had to build and install newer version of some libraries. Now I see multiple side effects such as Python is behaving weird (a package is installed but not visible to the interpreter), a software that I have removed totally is still being reported as present and synaptic is warning me of broken packages while trying to uninstall some things etc.
This is a recurrent and frustrating issue, after some time either packages break or become inconsistent.