Yeah, I almost exclusively only deal with 'problem' horses...though technically the horses aren't the problem, it was the human who owned the horse.
Regardless, not all trainers buy horses with issues and resell them after doing a bit of training on them.
You state that this is a 'new' horse. How new? It is VERY normal for a new horse to go on a string of unwanted behaviors after, what I call, 'the honeymoon' phase.
You have to understand that the horse is a herd animal. The horse depends on the herd to keep it safe. Whenever you take the horse away from the herd and environment it knew, there will be a period of time of adjustment as the horse tries to find it's way in the new herd. YOU are part of the new herd. Currently, you're having a bit of a power struggle. It's perfectly normal.
I don't understand why you were upset. The trainer is simply stating what he/she feels is the reality of the situation. It may or may not be correct. Perhaps you didn't like his/her tone?
Are you afraid the trainer is right? And that you've got a road of trouble ahead?
What I would do isn't relevant because I'm not you. So, maybe if you help me understand why you were upset, I could give you some additional advice that would apply to your situation.