The issue occurs only if C implementation of _warnings is available. It is caused by re-use of global filters variable from _warnings when warnings is being re-imported.
So warnings modifies _warnings.filters on first import. Then, when you import warnings again it uses already modified version of _warnings.filters and adds same filter for the second time.

I attach a simple patch that prevents duplicates in filters. I'm not sure if this is a best way to fix the problem, but it works. It certainly affects performance of filterwarnings(), but there shouldn't be a lot of filters anyway.

Making filters a set() will solve the problem also, but will require API changes. Although I didn't find anywhere in documentation that warnings.filters should be a list, someone might rely on its .append() method.