This is fairly wild speculation on my part, but I think Python is likely at the bottom of the suspect list for whose bug this is, after (in order):

1) your own code
2) matplotlib
3) Tcl/Tk

I would suggest trying to come up with the shortest reproducer you can (which should shine light on any bugs in your code), report your problem to matplotlib[1] with that reproducer attached, and link between this issue and that one so we can all keep track of it.  We'll keep this report open until somebody claims the bug.

Adding Serhiy as the resident Tkinter expert, in case you have insight I don't.

[1] https://github.com/matplotlib/matplotlib/issues