I did not have this problem with the Core Set at all. But I've moved onto Curse of the Crimson Throne and as far as I can tell every single CoTCT card has a different colored back compared to the core set cards. I noticed when I was shuffling two CoTCT banes with two Core Set proxies, it's different enough that I can tell which ones are the story banes without doubt. I double checked now that I've noticed it and I can also pick out all of the CoTCT cards in player decks, locations, and the blessing decks, just from the back.
example photo. The two on the left are the CoTCT story banes, the ones on the right are the core proxies.
I'm not sure what to do. Replacing an entire expansion seems like a waste to me, and I'm not even sure which one of the sets is actually off color. I'm probably going to have to unsleeve the entire box and do it over with opaque sleeves, which is a huge bummer. I'm loving the gameplay of the new version but the component quality has really disappointed me.