Yes, that map flagged as a river crossing and that battle being a meeting engagement has confused the game. What's happening is the AI troops are carrying the rafts to the river and launching them but not getting in. The "crew" of the raft is rowing them to the other side and then they sit there. The game doesn't know it's supposed to load the units into the boats because it's not flagged as river crossing right from the start.
That's the long answer. The short answer is don't do that
Don't use custom beach or river maps unless the battle type given to you is a beach assault or a river assault and then I still wouldn't advise it for those battle types because custom maps are rarely built with the AI deploy routine in mind so by all means use custom maps for anything
but the specialty battles and avoid custom river and beach maps altogether for any generated battle game.
Don