Sort of the same thing happened to me with my 4YO mare. She started fine, but after a few minutes of working, she would stop and refuse to move. I'd kick her or tap her with the whip (she is usually really sensitive) but she'd just kick and turn to look at me. She never really pinned her ears, but always looked annoyed. The first two times she did this, I got off and walked her around and gave her a couple days off. I was convinced it was pain of some sort. The vet found nothing wrong with her. Neither did the chiropracter, farrier or saddle fitter. Eventually she stopped doing it with less difficult work, less circles and trying to get her hind end engaged. I did a Stephen Bradley clinic a few weeks ago. We were working on gymnastics and towards the end, my mare just stopped and balked like she used to. Stephen got a crop and hit her so hard. I've never seen him hit a horse before and I've NEVER seen a horse hit that hard before. She had a swollen line from the whip on her flank and she was shaking. I was shocked, but he only had to hit her once and then she was an angel the rest of the ride.
I don't know if a good whack is what your horse needs, and there are probably other ways to get around this problem. If you want to try just one whack, you won't be able to get a hard enough hit from on top of the horse. Someone on the ground needs to get after your horse. My mare was completely fine and she wasn't sore or scared of anyone else afterwards.
Moral of the story- Your horse is probably pushing your buttons like mine (since the vet didn't find anything). My mare got stubborn when the work was too hard. Think about it- you were doing exercises that required balance and muscle. If your horse doesn't have enough strength (especially becouse he is young), he might just say "no" when he gets tired. Then, it becomes a habit because they know they won't have to do the hard work if they stop.
This was what worked for me, but if you don't think your horse will handle the hit well, or you're not comfortable hitting your horse DON'T DO IT. Find a trainer to help you work through it. It might just be a phase like it was for my mare; just don't let it become a habit. Good Luck!