I was wondering about the cabin where Coulson took Skye. We're told that Cap stayed there for a while after defrosting, we see an imprint from Hulk's fist on the wall and one of the "real S.H.I.E.L.D." agents called it "the house Banner built".
So was it the house at the end of The Incredible Hulk? But the walls look exactly like the walls on Coulson's plane, so it's S.H.I.E.L.D. tech. That would imply Banner stayed there some time after The Avengers (he had no affiliation with S.H.I.E.L.D. before that), but in the movie it seemed like he had control of the Hulk at that point, so the fist imprint in the wall seems weird.
So Banner built the cabin, S.H.I.E.L.D. appropriated it at some point as a safe house (or the safe house, as it's called simply "the retreat") and housed Cap there, then after the events of The Avengers Banner stayed there again and still had anger issues? Feels to me like the writers made it a little too convoluted with the little winks and nods.