It was scheduling conflicts...Cotto needed Steward training him the whole time and Steward just couldnt. I even asked Steward when I saw him at the airport a couple of weeks ago and he told me the same thing, that he just couldnt be there for the time Cotto wanted.
Here is what was reported by ESPN: http://espn.go.com/boxing/story/_/id/7059152/miguel-cotto-replaces-trainer-emanuel-steward Aside scheduling, some say there was disagreement about money.