MCU: Secrets and Lies

On re-watching Iron Man, and pondering Thor-1, it seems to me that SHIELD's knee-jerk reaction is to cover things up even when they don't need covering up. Consider the two cover stories they made in Iron Man: that Tony Stark's bodyguard is Iron Man, and that Stane died in a light plane crash.

( You don't need to be warned for spoilers for MCU surely? )