Yep, it's the pedal stroke. You're pedaling past the bottom of the stroke. If you push down at the bottom of the stroke, the pedal can't move down, so your body goes up. This inertia can bring the rear wheel off the ground. It's really inefficient and a waste of energy, so work on your stroke.

Swinging the bike aggressively to add power with your arms also helps with the hopping.