In one of the final scenes, Chrono is all business as he discusses what will happen to Fate now that everything is over... while Amy ties his head bandage into a bow and quietly Squees over how cute it is, apparently without him noticing. Then as the scene ends we hear "Amy, please redo it..." followed by her grumbling.
In the third Sound Stage, Nanoha shoots off some fireworks for Fate to celebrate the anniversary of her making a contract with Arf. Then it dawns on Yuuno that he never put up a barrier to prevent the magical use from being seen by outsiders, much to Nanoha's shock, and the two flee the scene in order to avoid being spotted.
When he does it, he turns to Nanoha, saying "It's been a while since I've been in this form, huh?", thinking he already showed her already. Then he turns all the way to find Nanoha completely gobsmacked.
When Lindy allows Nanoha and Yuuno to help them, Chrono is shocked about her decision and almost calls her "Mom", then he quickly changes to "Commander".
Also, her first meetings with Nanoha, where she is shown drinking Green tea... with milk and sugar like it was western tea. Nanoha fidgets the whole time, like she desperately wants to correct her, but that would be rude!
The Movie 1st
Another one from Chrono. After watching Nanoha and Fate seal seven Jewel Seeds at once - a feat that takes an incredible amount of power - his face is shocked, as though he's in awe... but then he says: "That was the sloppiest work I've ever seen!"