Yeah, the Discounted filter has been broken for months. I really wish GOG would fix this.

Incompetence (from the top down) seems to be a large part of it. :/

Fun fact: we are talking about lost sales because customers who filtered by "discounted" won't get to see some of the games that actually ARE discounted. So each day this isn't fixed you guys will lose money in further sales ... maybe it should be a priority for you to be able to sell as many games as possible ;)

That's the issue in the OP. It's been an ongoing problem since 2018, if not earlier. We also have the opposite: games with no discount showing up with the Discounted filter on.
I "solved" this by nearly emptying out my wishlist. I can fit the whole thing on screen now, so I don't touch the filters anymore.

I am aware that this was the issue the OP mentioned, just wanted to explain to GOG that they are damaging themselves by not making fixing it a priority - well, we all know how good GOG is when it comes to prioritizing things ;)

Empty wishlist - no need for filters ... yeah, not really a solution for me. I could as well stop buying games and would have solved the problem as well :D

They weren't even critically understaffed half a decade ago, were they? If they didn't fix it until now, what are the odds they'll finally get around to it? Well, don't let me deter you from trying to talk sense into them. I haven't entirely given up either.
I wasn't offering a workaround, hence the quotation marks. My point was the wishlist has been rendered so useless that I essentially stopped using it. I will revisit the situation in 1 year, but I'm unlikely to repopulate my wishlist even then. I've had enough of the e-mails/bell notifications for the same old discounts.

I think it's actually worse than that.
I use the wishlist for games that I am interested in, but not at full price. I presume that's the most common reason people wishlist items.
I used to religiously check my wishlist, 2-5 times a week. The filter made it easy to quickly find discounted games, and check if the price had fallen to a point where I would purchase the game.
Because the filter is double-broken (it includes 3x as many non-discounted games, AND excludes some truly discounted games) I don't use it at all, and instead manually scan the results. My wishlist is currently 3 pages long, so this involves pagination as well, which makes it more tedious.
I have almost certainly missed sales I would have purchased because of this.
Further, sales in any business are generally used to tempt customers into the store, in the hopes they will buy an unplanned product. I only look at my wishlist once a week now, so that "splurge opportunity" has fallen 2-5x for GOG for me.
It's bewildering that this has festered for so long. I write scientific software supported by massive databases. This isn't rocket science, and the fact it wasn't repaired in a week makes me concerned that GOG has staffing and/or financial problems.
I'm a Linux user, and love GOG, and have zealously used it in favor of Steam. I <am> on Steam as well, though, and their superior support for wine emulation thru Proton as well as a functional wishlist means I have been building up my wishlist there. It used to have maybe 4 products that weren't available on GOG, I've now added 50+ in the last month.

Right now GOG added a "Show only games on my wishlist" filter on the Store -> "On sale now" section of the website. This makes it much easier to see wishlist-only sales.

Wow, you're right, it was literally added in the last 24 hours (I reloaded a store browser page from yesterday and there it was).
I'm comparing the results to the "legacy wishlist". They differ at least in sort - it I sort the store page by "Rating (from highest)" and compare it to the wishlist sorted by "User Reviews", the order is significantly different. Not sure which visualization is correct, or if "Rating" and "User Reviews" are somehow different entities. Also I just learned you can't preserve the "Show only games on my wishlist" option in a bookmark (the loaded link will have the option checked, but not actually applied to the results - need to uncheck/check to take effect).

Thanks for this, though, I'll try using it rather than the wishlist.