I don't have this experience. Can you give an example of a previously-valid codebase that failed typechecking unexpectedly on a recent MyPy update, that wasn't a result of a false negative bug in MyPy?
But the big culprit is typeshed. Something will get new/fixed annotations and suddenly you aren't handling all possible return types in your callers, or whatever.
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).