Any time I put something a little too big in the trunk, the trunk lid/cover comes unhinged. Anyone have a good way to keep this from happening, but still allowing some flexibility?

Was thinking of fixing a rubber band to it somehow...

 

I wrapped the two "pegs" in ordinary black insulation tape, mainly to stop those hooks from rattling like crazy coz they are quite a loose fit over the pegs.
About 10 or 12 rounds of tape on each peg.
Works a charm, no more rattling, and the hooks sit nice and solid on the pegs, so much so that this might solve your problem as well.
One hint - you need enough wrapping to ensure a very tight fit, so tight that it's a bit of a struggle to now get the hooks back over the pegs, you now need to hold the bit of trim that the peg is attached to quite hard and then force the hook over the peg otherwise the peg and trim want to move too much, best done from the side of the car.

 

When I first got mine almost every time I opened the boot/trunk the cover had fallen off on one side just like that. The gap is too big so the mating hooks only just fit on both simultaneously. I fixed it by 3D printing a 1cm extension to the round pegs and screwing them onto the ends. (You could use matching size washers if more readily available.) A single wrap of Tessa fabric tape will hide the joint and prevent the rattle without binding.

 

Same problem here....my solution was to put a zip tie around each peg just to the outside of each hook. This keeps the cover from sliding from side to side.
CRA

 

Had this issue on my 2017 Coupe F-Type V6. Noticed this issue immediately. Had to take my car in a few weeks later for a recall check on the seatbelt tensior and might as well since I'm there, told the service writer about the issue. They went ahead and replaced it with a new one. Even the service writer admitted the pegs are too small and not long enough lol. So I recommend you go to the dealer and get it handled because haven't had any issue since.