Transmission repair issues

It was making a flapping noise when decelerating. Saved up and got it looked at, diagnosed as a cracked flywheel. $1,000.00 later it's repaired and the car gets a clean bill of health. Six days later, the car won't shift into any gear, but runs. Take it back to be told the transmission pump failed and I need a new transmission. I had bought a new transmission in October so it was under warranty. The warranty shop says the transmission is missing some support dowels that keep it stable and that's why it failed. They believe the other shop messed up when working on the flywheel. Who do I believe?