This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Wandering Son
The general concept of the series can be this. Transsexual children growing up.. Anyone who knows about Transsexuality and that age knows how horrible that time is, especially since most can't transition and the body changes.
When we find out that Anna broke up with Shu due to his "crossdressing". It comes off as a sadly realistic problem, and a Tear Jerker since they were so nice together.
And the Tear Jerker goes away when several dozen chapters later we see they've gotten back together and Anna doesn't seem to mind Shu's transgenderism
Nitori notices his voice is changing, when a girl tells him that. The look on his face, and the dull surprise, really throws you off. The anime went for a different response, with Nitori smiling and seeming to come to terms with the change, signaling that he's becoming comfortable in his own skin.
When Nitori gets in trouble, and becomes the laughing stock of the school, because he wore a Sailor Fuku to school even though he hasn't shared his wish to be a girl outside his small circle. Takatsuki got off scott-free, but when Nitori does it he gets sent straight to the Nurses Office. This incident also makes Takatsuki stop wearing the boy's uniform.
After having such a nice friendship, seeing Takatsuki's and Chiba's bond break down can be a Tear Jerker. They eventually rekindle though, but it took around three years in-series.
On a similar note, seeing Chiba's dramatic change in personality through the early volumes. She became dramatically more stubborn, aggressive, and depressive.
This happens a lot to Nitori. His haircut looking too masculine, going to the all-boys school, having to wear the male's waiter outfit at his new job.