Source: screenrant.com

5. What happened to the rest of SHIELD?

SHIELD was a huge thing throughout the first phase of Marvel movies. Until they were uncovered to be mostly HYDRA and exposed.

Yes, Coulson and his crew have been slowly rebuilding over on his TV show, but the original organization was gigantic. Impossibly so. Where did all of those people go? Some of them popped back up in Age of Ultron under Nick Fury's command, but that's not enough of an explanation. Even when we add up all the people who are still SHIELD, and all of the people who are HYDRA, and all of the people Fury pulled out of hiding, we’re still left with a huge gap.

SHIELD was a massive intercontinental organization. That required huge teams of people who are now out of work. At the very least, there's gonna be an unemployment crisis. And a huge supply of free agents on the market, killing machines looking for work.

In short, this is a bad thing. Someone should probably acknowledge it.