These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Isanami's unusual childish behaviour makes more sense when you realize that making her sad or afraid could make her disintegrate everything around her. Raising her in an ivory tower might have been thought of as a good idea.
In the manga, Anastasia's strange temporary clumsiness while dealing with Ichimaru and Niko during her introduction makes more sense once it is revealed they were actually working for the same guy at the moment.
Anastasia betrayal makes more sense when the initial purpose of the Braves were revealed: They're destined to die. She doesn't want to.
The biggest source of Ho Yay are probably Yukimura and Rokurou. They are extremely comfortable in each others presence and Yukimura is certainly more concerned about Rokurou's wellbeing than he is about the other Braves. This shows especially following the events of Episode 9, though they had fangirls squealing even before that.
Yukimura: Let's put the topic of whether it is a pathetic name aside. After all, there is only one Rokurou for me in this world.
The Scrappy: Isanami. It's hard to find a comment regarding the manga/anime in which someone doesn't complain about her. It doesn't help that she is also the ultimate Damsel Scrappy. During first four episodes of the anime, she managed to get kidnapped four times. Not to mention spending the final episodes crying. Not going to sit well.