2003 Dodge Neon SXT Transmission Problems

My Husbands transmission fluid looked like tomatoe soup and the transmission wasn't shifting like it was supposed to. He changed the fluid. He put in a new filter, gasket and Trany fluid. My father told him that some how he got water it the transmission. It wasn't anti freeze because that was full. The trany isn't still shifting. Its like its not going into gear at all now since the fluid got changed. What could be wrong? any comments are greatly appreciated.

cmh0382, the only ways I know of water getting into the trans. are a leaking trans. cooler in the radiator or running through some very deep water or the car being in a flood. As for going in gear make sure the fluid is full, checked while it's warm and running. Hope this helps.