Manga ch2 and anime ep 1. The anime has Kiruko and Maru talking about bodyguard and finding the place. While in manga, they talk about cannibalism.
Manga ch7 and anime ep2. The part where that one guy notices Kiruko looks exactly like racer Kiriko.
Anime doesn't have this "100%" confirmation from the guy, when both Kiruko and Maru denies about Kiruko appearance - identity.
Manga ch22 and anime ep8. Anime animates entire scene of Dr.Usami shoots himself, manga doesn't, but manga actually has a bit more happens after that. Kiruko experiences first period, I skip some pages so it looks very abrupt.

And then has to go to next chapter to see the dream sequence between Mimihime being lost and founded by Shiro, when this scene happens after ep8 credit.
Manga ch24 and anime ep9. Anime has Kiruko noticing bird logo immediately looking same as one on Kiru-beam gun, while manga has an entire back story about the gun prototype.
Same episode, but manga ch 26, when going through Dr.Usami old place, looking at the academy paper.
Anime has Kiruko remembers whole orphanage group while manga only focuses on interaction between Haruki and Kiriko, especially Kiruko has a bit issue with
self-identity.
And anime doesn't have this part where Kiruko asking Maru about cram school.
Anime episode 10 probably has the most deviation comparing to manga in action sequences and comedy delivery. Also, over the top goofy faces, all thanks to guest animator from Trigger studio. If I'm being honest, Trigger over the top animation style isn't good for this anime.
Adding more hints aren't in manga, like keychain between moms, Juiichi and baby.
And couple more short focused scenes on this guy.
Episode 11, bunch of flashing scenes around 12:00 where Mimihime is screaming, that part isn't in the manga but also tries to connect to Episode 8 between Dr.Usami
(Shiro) and the patient
(Mimihime herself).

[/ISPOILER]