Hi Evgeniy,
Assuming I have understood the problem correctly, it sounds like a request we already have on the todo list: WIP: How to exclude filter options which are not available for the current WooCommerce category? - #2 by timmse
Currently, the filter shows all data - no matter what you’re looking at. It doesn’t respond to the term you’re currently viewing. As I said, the request is already on the to-do list and we’ll try to improve the filter as soon as possible.
Unfortunately, you haven’t given me any feedback on your pagination problem yet 
Best regards,
timmse