Issues with ZoneDoctor...

So I've been experimenting with ZoneDoctor recently and I've been trying to learn events by looking at events similar to what I want and just copying them.

So I went to make a new event, only to discover that I didn't have enough space for what I wanted to do. So I was wondering where I could save space and I checked and decided that I didn't want Umaro to be recruitable - just an optional superboss if you decide to go for the Magicite and he'd end up being able to give you Mog's best weapon - assuming the moogle was in your party.

Anyway, I erased all of his script except the necessary parts to keep it functioning, and then saved. When I went back to edit new stuff there, I found that his script was gone and replaced by...one of Mog's scripts?! O.o?

So I tested this with other NPCs in the game and sure enough, if I erased stuff from their scripts, they'd just borrow stuff from another NPC or...even stranger, the program would get bytes in the negative instead of positive - as would be normal when you are deleting stuff to make room.

So my question is - does anyone know what causes this and how to avoid it? >.> Because it's annoying.