Basically, your wishlist (and maybe other pages as well?) display the sale % using the wrong number. It makes it look like you're getting a better deal than you are. For example, this game I wishlisted is $43.95 AUD. But if I get it in the bundle, it's $41.81 AUD. That's a 4.8% discount. But the wishlist shows 42% discount of the whole bundle, not the actual game I wishlisted. I think that's misleading.
You could argue I'm getting extra games so it's a good deal; but I don't know that other game, I haven't researched it or wishlisted it. In some cases, I've had this happen to games that are in bundles where I already own the other games. At that point I'm just getting completely ripped off, because it says 75%, but it's actually 5%, without even any "bonus games" to justify it.
To avoid this, never buy from the wishlist or home page or any page that isn't the original full store listing. I always click into each game to see the original store page and ensure it's a real discount before buying. I'd recommend doing the same.
I noticed this years ago and submitted a support ticket and a Reddit post, but it never got fixed. I feel like it must be by design at this point. This is the first "anti consumer" practice I've seen Steam implement.
There are two types of bundles, one where already-owned games are removed from the total price, and one type where they’re not. And in type two they even indicate that you’re not allowed to buy or gift the extra copy to/for someone else. Because of the lack of indication on the latter bundle type, it often looks like a steep discount when you’re really not saving any money