It could be that he is out of alignment in his back, or he could have been taught improperly how to pick up the canter, or he could be crossfiring, or he could be kicking out. Don't worry about it.
Just watch for other signs of discomfort; raised head, ear pinning, baring teeth, nipping at the saddle/girth/your feet, etc. If he doesn't appear to be in any pain, then it could be a hundred things that is causing it so don't go to stressing just yet.
Breathe!! When you have a chance, get some vid and we will be able to give some much better and more accurate suggestions.