How could you not realize a book that was giving you +1 skill point over and over and over again wasn't bugged? Are there normally permanent stat increases? I mean in Mario you can hit a block and a coin several times, then it becomes a solid brown block but that's usually not the case in RPGs without some identifier of charges.
The AI can't handle invisibility. I will give you that. But considering how silly rogues felt in Baldurs Gate I don't blame them for giving sneak some use (and I love the bush/rock cover too, they dont take it too seriously - how are you hiding in broad daylight). And invisibility, the general fix for this has been TRUE SIGHT for certain "bosses" or "dragons" and sometimes if they are "right next to you" you have them appear. I don't really care too much about invisibility, maybe just increase the CD on that and add some mechanics to sneak that you can only do it once per round - sneaking for 1 AP is nice and more important you still get the reduced line of sight from the skillpoints. I actually think that if Evelyn the first boss could cast invisibility on herself before the players first turn that would amplify the difficulty of that encounter.
You could also signify that things like stealth or invisibility end turn - you would retain the AP but you would not be able to participate until the next round.
I still think this is all just metagaming though. Blind has no save. I can teleport enemies into or away from my team at whim without them having a saving throw, and I can do all kinds of other things that they can't do. The important thing is I have all kinds of options, and while I could certainly cheese one or two of them, it's better than having one optimal play.
