At the end of Agent Carter, how come Howard Stark refers to SHIELD by its acronym, instead of its full name?Iron Man 1 made me think that the shortened name wouldn't have existed in the 1940s.
The name was only fully said in Iron Man 1 because it was the first movie to introduce the organization, and the general audience wouldn't know what the organization is and comic fans needed to know the acronym stood for something different. While the dialogue does make it sound like the acronym hadn't been invented until the end of the movie it seems to be Early-Installment Weirdness. As they hadn't fully fleshed out the MCU yet, and probably hadn't decided SHIELD would have been created right after WWII.
In the first movie Coulson was also depicted as a kinda wimpy bureaucrat rather than the Badass Normal that he is now. Definitely Early-Installment Weirdness. Or maybe Coulson just didn't know the acronym yet.
According to a tie-in comic, Fury never noticed that the acronym was SHIELD, and the agents avoided using it because they thought he disliked it. My own theory is that they initially used the full name because they didn't know whether they could trust Pepper (if she can't remember the name of the organisation, she can't repeat it, and people are less likely to trust her about the organization if she can't repeat the full name).