Transmission fluid in radiator - Coolant inside the transmission?

My sister bought a 98 dodge neon, with 120,000 miles on it. She need a new transmission for it, so she took it to a transmission shop. They got her one and installed it for 800 dollars. When she got it back she was excited and broght it over and wanted me to drive it. She just turned 16. Well I drove it and it shifted horrible it would rev way high before it shifted, and wouldn't hardly shift into 3rd. Its a 3-speed transmission. I told her something wasn't right to take it back to them. Well she just got her license so she didn't listen to me and drove for 3 more days. I guess it started to shift even worse. It would be in gear going down the highway and start jerking and stuff, then she couldn't even get it to go in gear. She would pull the shifter back to drive and it wouldn't move well after messing with it for a few minutes she got it to move and took it back to the shop. They told her there was water in the transmission. There was no problem with the radiator or anything where water could get in. They have no idea how water got in there. Is this transmission going to be bad now that it was ran with water in it for 4 days? They said there was only about a cup or so of water in there. They think a fluid change will fix it, but I think there will be internal damage what do you guys think? Thanks