Oh no! It's a good thing I decided to keep RPG Maker 2k open then (T~T)... I'll need to investigate those battles.
EDIT: Looks like the issue was that going into a tent triggered all of the fights at once... whoops!
EDIT 2: There's a weird graphical bug that might happen, but I cannot figure out why it's being triggered that way...
Also, that's good to know about EasyRPG! I'll for sure look into that!
Regarding the two other endings, I'll give you two hints:
1.) Pet the dog 500 times in the hut at the rebel base.
2.) Go to the big tent just before the airship theft mission and ensure you have a full party (yourself + 3 mercs).