It seems as though the opposing teams of Captain America: Civil War have been chosen, but if a recently uncovered deleted scene from Avengers: Age of Ultron is any indicator, rifts have been forming for some time.
The deleted scene, which shows an alternate take of a moment that made it into the movie, surfaced on a Russian Vimeo account. It shows a disagreement between Captain America and Maria Hill about preventative measures in dealing with Ultron and other villains. Check it out:
Avengers: Age of Ultron is due out on home video October 2, 2015, while Captain America: Civil War hits theaters May 6, 2016.