I just encountered this as well.  The way catch_warnings is implemented is a bit "dumb" in how it treats _filter_version (it calls _filters_mutated even if the active filters are not actually changed when entering catch_warnings).

More significantly, _filter_version is not fine-grained enough.  If some warning was already displayed, calling catch_warnings() should not later cause that same warning to be displayed again unless the filters were modified in such a way, during catch_warnings(), that that warning should be displayed (e.g. changed to 'always').

I'm not really sure what to do about that though.  Maybe the "filter version" should be per-warning?  Currently the value assigned to each warning in __warningregistry__ is not used (it is just set to True), so maybe that could actually be used for this.