flake8 and autopep8 both detect 'Too many blank lines (E303)' and 'Expected 2 blank lines after end of function or class (E305)' style errors. This causes autopep8 to ask if the autofix should be applied instead of applying it directly, and the flake8 errors will be reported anyway on phabricator as false positives even though it was fixed (if the linting happens as part of the arc diff command).
Making flake8 ignore those errors fixes this issue. Autopep8 will apply the autofix without prompting the user.