It's 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 in the past and sightings have become much more rare, but it is still possible.

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.

The Triple Tech Delta Attack (Crono, Frog, and Ayla) does not unlock in Jets. This is a known bug and is being addressed.

Update- Delta Attack has been fixed.