Entering/exiting certain rooms causes link to drop any items he's carrying, such as force gems or big keys. The ROM needs to be patched to handle this, or the logic needs to be updated to prevent this from happening (preferably the former).
To reproduce:
Checkout this commit e8eae15
Use faLSVeEigoLUrtZdUNeu as the seed
In the phantom hourglass pedestal chest in the ocean temple, there is a force gem. Trying to carry it further into the ocean temple doesn't work.