I don't use pyflakes much myself, but the maintainers of our CI system at work run it as an early stage, so if it complains, well, you know, nothing much happens. So, I'm starting to pay a bit closer attention to its output. To keep me from forgetting it, my Makefile's lint target now runs both pylint and pyflakes against a couple directories in my repo.
Running "make lint" today, I saw pyflakes emit messages for a file named utils.py.~1~, that is, an Emacs backup file. This is a new file in my sandbox which hasn't yet been added to the Git repo, so Emacs knows to create backups. (Once checked in, it will rely on Git.) It seems odd to me that pyflakes would decide to check such a file. Is this a bug or a feature? Looks like we are running 1.6.0, which appears to be more-or-less current.