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!"
The commentaries for the movie are filled with several funny moments as well.
Subaru has to explain to Teana the concept of Magical Girls and the fact that talking animals do not exist on Unadministrated Planet # 97.
Erio is unable to watch Fate's Transformation Sequence because he's embarrassed about seeing Young!Fate being naked. It gets funnier when Caro asks him which between Nanoha and Fate's transformation sequences interests him more. He starts to think about it for a while, before vehemently denying that neither one made his heart skip a beat.
Subaru and Vivio enthusiastically calling Nanoha's attacks, with added sound effects. They even treat Nanoha's "I want to be your friend" line to Fate as if it's one of the most iconic lines in the movie.
Subaru and Teana tell Nanoha about how her reputation as the "Ace of Aces" has somehow made Yuuno into a Memetic Badass in universe because of the simple fact that Yuuno was Nanoha's magic teacher. Nanoha thinks that this has made Yuuno's life kinda troublesome and decides to give him an apology later.
Nanoha reprimands Fate about her Photon Lancer Phalanx Shift destroying the buildings in the area during their climatic battle. Minutes later, everyone is horrified by the amount of damage caused by Nanoha's Starlight Breaker.
The Movie 1st Sound Stages
Vivio gets all worried that she'll never find her true calling in life because she's not lonely or confused. Nanoha can't help but laugh at her daughter's train of logic. Even though its audio only, you can feel the pout Vivio gives her mother.