Found one more.
In the area immediately past the Nekomata village when you get pinned down by a female nekomata and (if you repeatedly choose 'allow') fucked to zero hit points the screen goes black but the text continues and you can keep 'allow'ing further nekomata to fuck you.
Logically either you should black out and teleport back to the nurse's room or you should keep the graphics going.
P.S. Is it possible to get past that area? Because I have wiped out a dozen or two catgirls/boys with no sign of them slowing down.
[EDIT] Finally got past them.
Research items seem to disappear between semesters. Not sure if that's intentional or not, but it definitely happens. [EDIT] OK, it was intentional. Fair enough.
Minor Bug: When you research in the library and use a boring ladder it says you have collected one book from the start, then you can collect three more. You don't actually get four books - it's just the count that's wrong.
Minor Bug: When your Nekomata babies start walking around their name changes to NONE.
When the Nekomata caretaker 'takes care of you' your arousal (Heart) stays full instead of emptying.
After getting beaten up by werewolves I was left stuck in 'slow mode' the following day.
I don't see how to use 'brighten' in the main dungeon. The 'Skill' menu item is not usable, and you can't assign 'brighten' to a hotkey.
Potion Crafting is messed up. First, there is a 'potion' recipe listed of '-1'. That doesn't do any harm that I can tell, but then after you complete the first Metal Crafting lesson the '-1' entry turns into Reed Rope.
Fire 4 quest. You are asked to case Fire Bolt 2 twelve times in combat. However they don't teach you Fire Bolt 2 until later. Luckily he doesn't actually check if you did the assignment.
You can use the Comm -> Anya -> Spend Time together option to escape the waterways (probably dungeon, not tested) and wander around in combat mode.