Hey, I'm a big fan of the epic encounters and how much replayability it adds in terms of combat, so having this as compatible is quite nice to play with.
That said, I'm unsure if what I'm experiencing in some cases is actually intended, and I admittedly don't have the interest to go through combat without EE at this point just for testing.

As for the actual "issue", I feel like the amount of loot is... rather high. "Regular" combat seems fine, though from my very limited testing, is higher than without other mods as well.
So far, we've only gotten the "Survive-scenario" twice and "kill champion" once, but it gave ridiculous amounts of rewards each time. I'm talking ~4-5k gold and about 80-90! equipment pieces. Included in those being 5-7 artifacts (those being a EE specific quality).
Modliste includes Epic Encounters Core/Origins, Epip, Epip Gameplay, Derpys EE2 tweaks, Derpys Artifact Tiers, Epicer Enemies, Pips Roguelike Arena EE Patch. In that order.

I'm half expecting derpys EE2 tweaks to be the culprit here, as it rebalances/increases overall amount of loot to balance the removal of lucky charm.

And another issue, though unsure if an actual issue or related to the loot thing; it feels like the game throws a lot of enemies at us, far more than "most" encounters in the base campaign do. I think about 8-10, each combat aside from the first few?
EE gives the Lone Wolf talent by default, so even when playing with 4 characters it's there, even if it doesn't do anything. Not sure if that leads to an overly increased amount of enemies, or if it's intended.