I've had this problem a few times., For example it happened with the 0.800+ versions. Mypy got stricter, and was more aggressive in finding code (eg small scripts in not in the proper python hierarchy).
It's hard to classify anything as a "false negative" with mypy since it is very liberal (often unexpectedly so, which I think is one of the sharp edges of gradual typing).
I can't show any of my professional work (no publicly available src) but this side project of mine is locked to 0.790 until I can find time to sort the issues: https://github.com/calpaterson/quarchive/tree/master/src/ser...
It's hard to classify anything as a "false negative" with mypy since it is very liberal (often unexpectedly so, which I think is one of the sharp edges of gradual typing).