I know in my T-9 I was having issues but it was easy to solve. The shape of the ship causes the prospectors to slide along the belly until they clear the nose. Due to the T-9's tokyo-drift method of maneuvering, I was firing a prospector while the ship angle was still changing and it was colliding every time.
To solve it, I got better at flying. I only fire the prospectors now when I've got no lateral movement, or, if I do, I immediately use "up" thrust after firing to give the limpet clearance from the ship.
Took some getting used to, now I don't notice it.
As for the OP's statement about losing drones in the cargo bay, I have no idea what that's about unless you're moving "down" while the limpet is bringing cargo "up" to your bay and you're smashing into the collector limpet.
Hope this helps.