On a positive note, we had a horrific incident with a 3 year old pony who ended up getting a front leg tangled in a hay net (you'll never find another haynet in our possession), flipped himself and get wedged underneath a divided in our trailer, while hanging from being tied. We had to cut the rope, keep him calm and have people help us get the divider out so he could stand. He never associated it with a bad trailer experience, and the next time we tried to load him, he marched right in with zero issues (and to this day has never had issues).
We also had a bad incident with Shay-las Clyde/TB cross mare as a yearling when we tried to tie her and she FREAKED out, got her legs slung over the divider and fell down. We also had no problems with her the next time we had to haul her as a baby.
So just stay positive and you'd be amazed, as babies, a lot of them bounce back both physically and mentally!