It's not the gasket that is the problem.
Hatch seals are not symmetrical and sometimes get twisted. The composite picture below shows on the port (red), a seal that has twisted out of position.
This tends to bind that side causing it to hang up. Making sure your hatch seals are correctly positioned is the first step in correcting an uneven hatch.
Your kayak is a piece of plastic that is going to warp in the sun over a period of time.
Interesting. I haven't seen this issue come up before. None of my Hobies over the past 13 years have suffered any twisting, warpage or lack of symmetry. Understandably the boats expand and contract with temperature and can dent with too much local pressure on the hull, especially in heat. But then, mine are stored inside usually and tend to be the lighter, cooler colors.
So while this may happen in some circumstances (as in your case), it's certainly not a foregone conclusion IMO.