After playing it some more, I managed to pass the jellyfish. However, there is still semi-occasional crashing in other battles I've had in the forest during combat along with the jellyfish. It never did that before when I first started to fight things. As for fighting them previously, I didn't mess with them too much until gaining better equipment.
After your tip, I went and tested it and it has been confirmed that using “Fast Atk” with “Knuckles” equipped will cause the game to crash.
Other weapons have been tested differently depending on their effects, and no serious issues have been found yet, except for the “Dagger” and “Kite Shield” effects which do not trigger stuns and sound effects on enemies other than the target.