Surprisingly enough, moments exist even in this mostly feel-good of series.
- Prior to being adopted by Koiwai, Yotsuba went through Parental Abandonment of some sort as a baby in another country. It's no wonder Fuuka and Ena are horrified when they first find out from Jumbo. Luckily Yotsuba doesn't appear to hold any memories of that time nor cares about her life pre-Koiwai - she's more than content with her current family as it is.
- In the first Festival Episode, immediately after being told to stick together, Yotsuba lets go of her dad's hand to run up to a cotton candy stand, thus losing him in the crowd. She looks desperately around for her father, gradually getting more upset until she starts to cry and shouts, "My name is Koiwai Yotsuba! My name is Koiwai Yotsuba!" Thankfully it's only brief as Koiwai had purposely hid from her to teach her a lesson about not listening to him, and comes back as soon as she cries.
- Chapter 68 is a bit dark for Yotsuba&!'s standards, as it deals with her lying about breaking a plate and Koiwai's rather frightening punishment for it: taking her to a temple and "trapping" her with the Nio statue so it can get the lying-bug she allegedly has out of her. The Nio frightens the hell out of Yotsuba and she is eventually reduced to tears, scared it will eat her.
- Chapters 75 and 76 deals with Duralumin having his voice-box broken and Yotsuba depressingly waiting for him to get fixed. Everyone is surprised by how down she is, to the point that even Yanda makes an attempt to cheer her up.
- Chapter 88 deals with Grandma leaving her son and granddaughter to go back home. Yotsuba takes it badly and refuses to let her go, even going as far as to hide her luggage and dress up as the alleged black monster in her house to stop her. In the end, she breaks down crying and hugs her grandma.
- Chapter 108, while a mostly pleasant outing to get Yotsuba a randoseru,note includes a flashback about Koiwai talking to his friends about the day he realized he was a father. It only clicked for him around Yotsuba's toddler years, when she began walking and following him around calling him "Daddy". Remembering that conversation and that moment while watching his now five-year old daughter prepare for school makes him choke up, as did many readers.
