From what I've been reading this is what most likely happened:
It appears that the monorails were approaching the end of their operating day and that Monorail Pink was attempting to reposition itself to go back to the monorail barn for the night. For Epcot monorails, this requires leaving the TTC station and passing a track switch, then backing up to the Magic Kingdom Express monorail station. Once fully on the Magic Kingdom Express beam, the monorail continues in reverse past the Polynesian and Grand Floridian resorts and the front entrance to the Magic Kingdom before it backs up through another track switch that takes it to the monorail barn.
The pilot of Monorail Pink was apparently backing up, thinking that the monorail was heading for an empty Magic Kingdom Express station, but the switch had not moved to transfer it, and so Monorail Pink backed up into the Epcot station that was already occupied by Monorail Purple, which had already loaded and was about to depart the station when Pink slammed backward into it. Since the collision system is reportedly disabled during track switching, there would have been no automated warning. Because the curve on which the Epcot/Magic Kingdom Express switch is located is quite dark at night, and the tracks curve back into the station, it would have been very difficult for the pilot of Monorail Pink to visually notice if he was on the wrong track. There has also been an unconfirmed report that there may have been some miscommunication between the monorail shop and the monorail control center regarding the position of the switch which, if true, could have meant then the monorail control center would have given Monorail Pink the go-ahead to reverse through the switch and back through the station while the switch was still connected to the Epcot loop.
The monorails have a fail-safe system called MaPo that prevents two trains from getting too close to each other, and actually applies emergency brakes if a driver tries to continue through a warning. However, both trains had had to override their MaPo warnings as standard operating procedure for the maneuvers that they were attempting to undertake. In order for Monorail Purple to enter the station while Monorail Pink was still engaging in its switch procedure, Purple would have had to override its MaPo shutdown. In order for Monorail Pink to reverse through the switch, it would also have had to override MaPo, as the track switches automatically cause a MaPo alert. While in override mode, the maximum speed of each monorail is 15 miles per hour, whether moving forward or backward.
