Yep, doing the lighthouse after the night scene with Jasmine causes the battle to start with Magnemite at 0 HP. The hp_magnemite value isn't being reset in between scenes like it should. It's a bug that'll be fixed next update.
Breaking into Jasmine's house leads to some bad karma options. If you talk to her in the gym you can warn her that having the key in a fake rock is a bad idea, but this doesn't really do anything big for the rest of the story. If you talk to her about the info on her computer, you can convince her that it's mortally repugnant, but this also doesn't really do anything major. Maybe I'll add some more stuff stemming from this. I could have some non-villainy side effects of breaking into her house but I'm not sure what they would be. Breaking in is already sort of villainous, I think...
The scene with the fanboy only has the options to either say nothing or to be a jerk. Upon reflection, there should probably be a third option there. I'll come up with something. Maybe something like "Politely make an excuse for you to leave so the fan doesn't annoy her"
And thank you for the kind words!