Transmission Problems

I have a 99 Cherokee. The transmission was just replaced, on the way home the new transmission completely stopped shifting. The shop is taking it back in to fix the problem, they said "it may only take something simple to make it work". What are some possible causes for this to happen ? Could the busted transmission have been misdiagnosed in the first place and now the jeep has the same problem ?, if so any ideas on what that problem could be ?