I'd say the negatives in his behavior were being inflexible and TOO by-the-book. It seems like an experienced field ops agent would learn to use the assets of his team better, rather than just shouting at them. On the other hand, I doubt the his field teams have ever consisted of a stretchy guy, an alien in a monkey suit and a woman who can turn invisible and project force fields. So he's not handling it as well as he could.
Hawkeye has the movie role of the cop who catches the film's hero in the warehouse and makes stop disarming the McGuffin and makes him put his hands up, and the hero is trying to explain how it looks odd, but really it's okay and unless the cop lets him go right now, then entire planet will explode (or whatever. You get the idea.) You, the audience, KNOW the hero is telling the truth and are annoyed with the stupid cop for stopping the hero. Whereas what the cop is doing is actually extremely reasonable, given the circumstance.
No one gets what I'd call terrible deep characterization here, everyone pretty much acts like a stock sci-fi movie character (except Sue, maybe), but for light 'n' fluffy (ignoring all the dead aliens), it's all pretty amusing.