Help with monster sprites

Recently I started working on creating my own enemy hacks and got ffse (ver 2.11) to change monster sprites. One thing I noticed early on is that if I try to replace a sprite with a new one and the new sprite's dimensions exceed the original then the new sprite looks messed up when I play the rom.

One way I tried to get around this was by using an enemy who's original sprite was at least as large as the one I planned to replace it with. I then tried using FF3usME (ver 6.5) to change the monster formations so I could fight the new enemy I made. However from the looks of it, the sprite still gets messed up unless one of the monsters that was originally in that formation had a sprite at least as big as my custom enemy's sprite.

For example suppose I replaced Atma's sprite with a monster sprite that was 100x100. Normally that would look alright since the new sprite doesn't exceed the original. However if I then replace the Hadesgigas (enemy in zozo) in the formation where you fight just one of them by themself with my new enemy it gets messed up.

Sorry if this sounds confusing but has anyone else encountered this before and if so is there a way to fix it?