Hi Veronika
I had another look. This issue is very confusing.
What I can see is some very strange behavior – and I think its a conflict with your theme + S&F.
Basically the meta variations now don’t work, because they are part of “variants” and in S&F you have only “products”.
If we enable “variations”, then categories filter doesn’t work.
I think what happens is, when there is a search for “products” + “variants” your theme (or another plugin) jumps in and makes some strange modifications to the query, which cause the unexpected results.
I cannot think of many options left except 2 (sorry but you need to do this to continue):
1) Disable all other plugins except content, woocommerce and S&F
Do you still get the issue?
2) Try another theme, just temporarily..
Do you still get the issue?
I bet, after one of these S&F will work normally, then we know where to investigate and I can set up a dev environment locally.
Thanks