Hi!
It is very hard to tell without actually seeing the issue directly, but I have a few guesses:
1. By default, the plugin shows items that does not belong to any taxonomy. Make sure to turn off this option, if you don’t want that to happen: https://i.imgur.com/rDbBbhj.png
2. It is also possible, that changing the default filter logic may give you better results. Try changing this option to ‘At least one of the selected terms should match’.
3. Also, make sure that under the General Options -> Sources 2 panel there are no taxonomy terms selected to be returned as results, as the filter does not affect those: https://i.imgur.com/1JS1G9c.png
Let me know!