Is water coming up over the top of your deck at all over the course of your outings? I have noticed with my Malibu Kayak, which has hatches that don't seal all that well, that if water comes up over the top I'll get a small amount of water in the hull. If I'm cruising around the bay and don't take any wakes I'll have a dry interior until I hose it down at home.
What you are experience might be "normal" water ingress. Maybe rinse off the kayak at home and see if water is getting in?
Try to deal with the scratches, because they'll just be back. I have heard that warming them up with a heat gun might smooth them out. I have scratched off the burrs from deeper scratches with my thumbnail and just dealt with the rest.
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