I use local python interpreter, pep8 work well and I see all warnings in my files. Then I switch to remote python interpreter from Docker, all warnings disappeared.
Python on local and Docker: 2.7.12
Pycharm: PyCharm 2017.3.3 (Professional Edition) Build #PY-173.4301.16, built on January 11, 2018
As explained here, Pycharm needs a local interpreter in order to inspect the code. For me, the following worked:
Basically my understanding is that it needs a local interpreter to be configured for some project but not necessarily for the specific project you want to run the inspection on.