As a programmer myself I wonder why is this game so buggy? The game looks like could be made in a very modular way, since the girls always have the same scenes.
Because Oni's not a programmer. It looks modular and Oni's doing the best he can, but because of variable naming, a lot of copy and paste code, among other things, when he's implementing new features or adding new things, he has to touch a lot of different places. Things can get missed, typos happen, conditions has to be modified and might be wrong, etc. Honest, for a non-programmer, the code isn't bad. But it really does show that Oni isn't (nor does Oni intend to be) a programmer.
With that said, use rpatool to extract archive.rpa some time. rpa is just an renpy flavored archive. Once you've extracted that, you can read (and modify) the plain text renpy/python code.