You no longer get free upgrade levels to Quark Upgrades for which you've unlocked the right to buy them, but have not yet bought any levels.
"Cube/Tesseract/Hypercube to Quark" Quark Upgrades no longer give a flat 50% per level. It was found to be overly powerful. Now, you get up to +50% Quarks as an additional bonus based on free levels. The first free level gives +5%, then +4.5%, etc... the increase per level exponentially decays.
"The Gambler" Ambrosia Module now has a max level cap of 40, instead of 25. Its base cost is halved so its final cost is close to the original (though still more expensive)
Fixed Red Luck Quark Upgrades having the incorrect Shop Typing.
The third Red Luck Quark Upgrade in the series now has a double free upgrade modifier! This means all free upgrade levels for this Quark Upgrade are doubled!