All along I was assuming the Ultron drones were already constructed prior to the movie beginning and would turn evil halfway through. So I was assuming the mystery cargo in Gonzalez' Helicarrier was going to be Ultron drones and the Theta Protocol was activating them. Now I have no clue what it could be. A mothballed Helicarrier or a facility with nobody in it doesn't make any sense and we already knew about the Index. Unless it's drafting all the superhumans they know of...
I was also shocked to learn in the movie that the Avengers have been working together for quite some time going on Hydra raids. You'd think they would have mentioned this in the tv show since this season has been all about going after Hydra! I was assuming they only meet for the second time ever in the movie.
Didn't the last episode end with Coulson telling the Avengers (through Hill) that Hydra had the sceptre? Which then leads them to start the search that ends in AoU? Maybe I misinterpreted something, but at the end of that episode my immediate reaction was: 'Oh, so the movie is actually a couple months ahead of the show's timeline here.'