Always save before entering Proto Dome. There are many ways to softlock inside, most having to do with the game expecting different things from the cutscenes inside which Jets has altered. It is safe to engage the enemies at the beginning, but after you pick up the character, do not open any menus (X or Y) and do not use the Enertron. Leave via the front door or through the Gate to End of Time before you perform any other actions.
Sometimes, a strange text error happens that will show an enemy or boss dropped a “WoIflobe sword”. This is a known bug even in vanilla! The text will be distorted and won't actually read as words. This causes no issues or problems, and the correct item is still added to your inventory. It is often a high tier weapon, so it may be worth double checking your equipment!
The Triple Tech Delta Attack (Crono, Frog, and Ayla) previously did not unlock in Jets.
It was possible to get frozen in the whirlpool after Heckran Cave on the overworld map. This glitch is rare. If it happens, save the game and reset and the whirlpool will spit you out. This bug has been addressed by the developers and is believed to be resolved. Please let the developers know if you see it.