This has happened a few times to me. I got the hump and took the luggage cover out to have a good look. There is a very small lug which holds the spring in, so to ensure it caught properly I pushed the spring clip in with a small electrical screwdriver to ensure it was properly seated. Has not popped out since so am hoping this has cured it.
Noticed the same problem this morning for my partner's car - it was the LHS clip when you look from the back of the car.
Are there any special techniques required to remove the cover from the hinge plates held down by the screws at the back of the luggage recess? A quick look this afternoon didn't give me a clear idea of how the cover could be removed - the owner was looking over my shoulder to make sure I didn't do any damage so I couldn't be too adventurous.