While browsing through the store, I just noticed that I had 3 items in my wishlist. Since I only remembered wishing 1 game, I was curious about the remaining 2. It turned out there really was only 1 game in my wishlist. I've attached a screenshot highlighting the problem.

My guess is that the other 2 games are games that I have purchased after wishlisting them. While it makes sense to remove them from my wishlist, since I already own them now, the count should also be updated appropriately. Instead of "3", it should say "1", because that's how many games are left in my wishlist.

I also tried to fix this on my end by going to the games' store pages and remove them from my wishlist from there, but the wishlist button is missing (which also makes sense), leaving me with no option to remove these games from my wishlist.

Is there anything else I can try to have those games properly removed from my wishlist?

The numbers in the user menu at the top of the page have been frozen for months. If you log out then back in, they should disappear altogether.

Logging out and logging back in did indeed remove those numbers entirely. It's not quite what I expected, but having no numbers is better than having the wrong number.

Thanks a lot for the help!

You're welcome. On January 5th, Dev0_NZ posted a solution (for GOG to implement) but neither of us managed to get a response.

If anyone wanders in here looking for a related issue, I posted how to remove invisible wishlisted games in another thread.