First of all, great work! This hack looks to be trully huge and adds a lot of fan flavoring to the game. I'm really enjoying it.
During my play so far I have seen three very small bugs during battle transitions (I don't know if they are caused by the hack), I'll try to explain them in case you want to check them out.
The first bug is very straightforward: right after using the teleporter for the first time (and before Marle tries using it), you can walk right through Lucca's father - but you can still talk to him if you position yourself properly.
The second bug happened in Guardia Forest at 600AD. There is a place with two hidden treasures (the shiny blinking dots). One of them lures some enemies (it's a trap) and the other has a power tab.
On my playthrough I checked for the one that lures some enemies first, which started a battle. When the battle ended, the sprite for the other hidden treasure briefly showed "Miss 89" instead of the shiny dot for about a second then reverted back to the shiny dot.
The last bug happened at the Cathedral where you rescue Queen Leene. There is a spot in the main hall where you have to fight two Nagas and they call two other enemies (called Devils, perhaps?). The Nagas stay at the top of the screen and the two Devils at the bottom.
However, when transitioning to the battle the bottom right Devil glitched out and disappeared. After I killed the other three enemies and the battle ended the Devil reappeared, but couldn't be interacted with.
For reference I'm using the 64-bit version of Retroarch for Android with the Snes9x core.