I assumed they were the entirely poppable bubbles that Garnet, Amythest, and Pearl used to capture most of the gems before Steven was allowed on missions. Remember how easy they were to pop? As Xenonia says, Steven just fell on one and it burst.

And honestly, sonic attacks are really dangerous to start with. Especially ones strong enough to stop projectiles in their tracks- that requires meeting them with equal force. It's kinda like hitting a brick wall. So there's really three options here: Bubble's invulnerable and the sudden stop catapults the gem against an indestructable wall, the sudden stop carries inertia and the Gem shoots through the bubble anyway, OR the bubble's popped by the impact of the sudden sound and the gem's flung backwards from the sudden force.