One thing i have noticed in Avengers fiction, which is especially agregious in this day and age is the abuse of the tech McGuffin, and this is more a issue related to Tony and JARVIS. It probably only annoys me so much because I work in the tech sector, but Tony and JARVIS are apparently an unstoppable Skynet/Big Brother/scares the hell out of me that an asshole drunk has that much power. I mean he hacks everything, regardless of open/closed system, access, whatever. Despite the fact he clearly had to be invited onto the helicarrier in the movie to even get into SHIELD's systems. There are limits even in fiction, or at least a reasonable explanation needs to be forged for how Tony can hack SHIELD's database whenever he wants when he couldn't even stop Coulson from hacking JARVIS with a phone while stuck in an elevator.
The second point is more to the Hawkeye/Widow/SHIELD side of things, having been around some military and intelligence projects on the tech side, and even just from watching documentaries and what not, the talking over the comms or while on mission is completely unbelievable and incredibly casual/unsafe. No ever uses a call-sign (not code name), or the NATO alphabet, hell, no even ever says over to sign off or uses military slang. If someone were ever listening in, well, it's all out there in plain English. more writers should look to something like Generation Kill as a good example of proper field communication, rather than just have Coulson and Clint chatting away like they are sharing a beer with no regard for mission protocols.