These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Edna & Harvey: Harvey’s New Eyes
Angst? What Angst?: After Lilli learns the truth on what she had done to her students, she finishes vomitting and departs the bathroom without saying a word. And yet when you control her again, she looks no worse for wear.
Fridge Horror: Lilli finds the chair leg that Edna used in the previous game and uses it to fend of the phantom. However, Edna can actually burn the chair leg, basically screwing Lilli.
Family-Unfriendly Aesop: On first glance the hypnotic restrictions made on Lilli make perfectly sense and is somewhat Truth in Television. Most parents teach their child this commandments eventually (hopefully more subtle). But then it turns out that the restrictions are causing more harm to Lili than good.
At the end of the game, all the stock aesops have eventually been deconstructed or outright broken.
Hilarious in Hindsight The Rabbit defending the not going into dangerous places block cites as one of the places a child could be safer than wandering around the village after dark is a Rolf Harris concert, he is currently awaiting trial for child sex offences.
Values Dissonance: Sure a cave can be a dangerous place as well as going out at middle of the night. Yet the rabbit apparently sees nothing wrong with a little girl walk into a BAR at the middle of the night to get drunk. Granted it does shows up when she attempt to drink alcohol but at that point she would've been in huge danger already.
Something the bartender lampshades immediately after Lilli walks in, mentioning that all kinds of horrible things can happen to a little girl walking into a bar with a man in it.