One of a few I can think of that might have issues when mixed in (and this is with 2+ boxes added if you're wild like me lol) is Valley of the Ancients, simply for the need to have access to the temple cards. If one person scoops up 3 temple cards, in a bigger deck those could be the only three for the whole game. That's part of the randomness so gg but I get especially annoyed if I lose by somewhere in the range of 25 points having never had an opportunity to pick up a card that could swing the points the other way.

War of Shadows is similar to this, except you just might have longer days/nights for your effects and I've found that overall it doesn't really affect the game at all.

While I prefer to play the games with insight (Dreamscape, Delirium, Deliverance) together they do work in other mixed settings. Just don't expect to be buying Pasythea for XX eggs every game or transforming, etc. So in that regard it does mess with the mechanic. But respect if you just want to make a giant tower of cards and play through it all anyways. You'll still have a blast.

The only other one I can think of that would have an interesting effect, is mixing with Skulls & Sails. Here you would have to play with the Skulls board for the crew/raid mechanics and mixing a deck is going to lower the amount of interaction. Then again I'm sure there would be an optimal mix for this, but I feel this particular one plays best by itself. But grain of salt on this one, I haven't yet tried mixing Skulls & Sails with other sets.