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.
Even Better Sequel: Or in this case "Even Better Spin-Off". While The Breakout is equally beloved by fans, one could make the argument that Harvey's New Eyes improved on a lot the first game's aspects, and both Lilli and Gerret are treated just as importantly by fans as the title characters.
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. As of June 2014 Harris has been found guilty of offences involving girls as young as seven. He is currently awaiting sentence for a string of child sex offences, many of which involved trusting young fans.
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.
Yandere: Lilli of all people is subtly implied to be one during the first chapter. For context, the game hints that she has a crush on Capu, who looks like he's about to admit he likes her as well... only to ask if she can deliver a letter to Shy for him. The narrator tells us that Lilli had always been envious of Shy for being the prettiest girl in the convent. The fridge horror kicks in when Lilli accidentally kills them both to retrieve the firecrackers. While not intentional, it can be read that she unconsciously murdered them both out of jealousy.