When the kid from Community first showed up on screen, they mentioned something about someone in Afghanistan. I didn't catch the beginning of the line but I assumed it was explaining where someone was.

But overall, I think it's just going to have to be something that people need to overlook. I had a bigger issue with it in Thor than this one but you're right that it's more problematic since SHIELD was in this one. I've just grown to expect logic gaps (like why Frank Grillo didn't just kill Cap once they secured the ship in the opening scene.)