Episode 1, Shino adjusting Tsuda's tie, and administering punishment for violating school dress code simultaneously.
In one episode, Aria is putting some boxes up on a high shell, causing her breasts to jiggle. Shino and Suzu comment that they look heavy. A moment later, Aria is carrying a heavy box, and Tsuda tells her that he'll carry them for her. Aria immediately misinterprets the object he intended to carry for her as her breasts, and complains that it's sexual harassment.
Uomi: Your hand is really soft, too, President Amakusa.
Shino: I thought I wiped the *censored* juice off, though.
Episode 3. Shino feeds a deer, which then licks her hand for crumbs. She and Aria comment on how pleasurable it is to be licked, causing the herd to Sweat Drop and look at them.
The second season version ends with Tsuda confronting everyone he spoke to that day, attempting to weed out the person who framed him by checking their alibis. (With the audience asked to see if they can figure out whodunnit with the clues that only one person there is guilty, and only one is lying.) Suzu and Kotomi are nervous wrecks, Aria claims she was busy in the bathroom due to an enema but did get out the sex toy, Shino plays it cool while casually mentioning that she has a D-Cup, and after all that, Hata outright admits it was her, laughing all the way through the closing title card.
In Chapter 90.5, there's a short omake where the crew talks about how they're going to be animated. This exchange occurs:
Shino: We should decide on a tagline for the anime. How about "a heart-warming slice-of-life anime"?
Tsuda asks the girls not to stare at him so closely ...so they decide to watch him like Yanderesinstead.
Uomi's tendency to say outlandish things perfectly calmly leads to a lot of laughs. For example:
Uomi (on seeing the Ousai Council out together): Oh, a girls' day out?
Takatoshi: Er...I'm a guy.
Uomi: Oh, darn... I gave away my plan to dress you up as a girl.
Takatoshi: Now that's scary.
Other occasions include the time she was waiting for Takatoshi at home, and notes she was waiting while wearing nothing but an apron but it got cold so she got dressed.
On one occasion, Uomi is staying overnight at the Tsuda residence alone with Takatoshi. The next day, Shino mentions she called but no one answered.
Takatoshi: Oh, around that time?
Uomi: We were probably...
(flashback of Uomi and Takatoshi in the bathroom, where Uomi is explaining the benefits of a milk bath)
Uomi: In the bath together.
Takatoshi: That's true, but not true!
The misunderstanding that happens when Mori, Uomi's Vice President (and her school's equivalent of Takatoshi) visits and the girls eavesdrop on their conversation:
Mori: Do you have any requests for your bento tomorrow? (Unbeknownst to the girls, she's delivering a message from Uomi.)
Kaede's Oblivious to Love moments with Takatoshi. For example, when Takatoshi praises her and says what a great person she is, she blushes and feels her heart racing... and concludes that talking to boys is bad for her heart.
In book 12, she is unable to find a seat in the library and asks Takatoshi if she can sit next to him. Right as she sits down, everyone else at the table leaves and she realises the situation makes it look like she just wanted to sit with Takatoshi.
Later, she is asked to help buy some male underwear by her older sister and recruits the Student Council to help. Takatoshi offers to accompany her to pay for it, and she accepts. She belatedly realises that it makes it look like the two of them are a couple going underwear shopping together.
The former Ousai Student Council President Furuya-san is so old fashioned, it's hilarious. When she first meets Suzu, she offers to help with the calculations. Suzu moves to get her a calculator, but Furuya-san tells her she brought her own. She then proceeds to pull out an abacus.