Continuity mistake: When Danny is about to dress his knife wound, he grabs the tape with both hands and there's nothing covering the wound. He tears the tape, still using both hands, but then in the next shot as he's putting the tape down, a gauze pad is now covering his wound.
Continuity mistake: When Danny and Ward meet Joy in her new place, Ward says "who was it who said I was being childish?" Danny is in the background, holding the folder cover open with his left hand. Shot cuts as he speaks, and his hand's suddenly on the pages with the folder cover hanging down loose.
Answer: Sokovia is a nation in the Iron Curtain. It is just as likely for a US operative to end up there as any of the other former Soviet nations. There is no reason to believe she was there at the same time as the Avengers. It was likely some form of covert mission there years beforehand.