Motto! episode 10, full stop. In this infamous episode about puberty, Naomi feels embarrassed about her breasts growing. And there's also the part where Reika flaunts her chest and gets her bra snapped off by her own teacher (Miss Seki) during the health exam.
Dokkan! episode 19 is full of this. Hazuki being a Covert Pervert? A little boy running onscreen with his genitals exposed? Hmmm.
In Dokkan! episode 13, Onpu deliberately gropes Mutsumi's breast to show her that boys are uncomfortable with touching her body. Later, Mutsumi makes a rather suggestive remark about Hasebe encouraging her to wrestle.
Despite that it was sung by a bunch of adults In-Universe, the insert song, "Namida no Broken Heart", has some racy sexual imagery in its lyrics about a summer fling...
A teary broken heart from last summer
Your figure... it's sexy
Even if you let me make love to your bare-naked body
You're so cool about it... I'm mesmerized
Did we also mention that Takurou Hagiwara, a 12-year-old boy, gets to cover the exact same song on the class 6-1 Image Song album?
Na-i-sho episode 1 has a lengthy scene of the boys doing their business at the urinals, even going so far as to show them finishing and zipping their flies.
Some episodes have nudity used for comedy, odd closeups of lower areas (male or female), episodes mentioning puberty and even double entendres.
Reika Tamaki in the first Non-Serial Movie ends up wearing a sexy Playboy Bunny suit when the Witch Heart Flower messes with her wish. She was 10 years old in the movie.
First season episode 46 has a Male Gaze close-up of Majo Rika and Majo Ruka's breastplates when they're practicing their samba dance, complete with lots of Gainaxing. Probably counts as Fan Disservice, as both were witch frogs at that point.