Sorry for that inconvenience. I think it might have happened when you pushed them in, maybe a bit with the rear part. To check, press them in again and screw them down and see if the rear part of the fin really "enters" the cuts or if it stays right on top. It is supposed to be a perfectly flush fit. But margins are tight. So a safety measure that really will not effect performance is to angle the upper rear part away from the board a bit with a file or some sand paper.
As for the particular questions.
1. There is a lot of fiber around there, but as a safety measure put a drip of superepoxy or something in the cuts. Even some ding stick will work.
2. I think the fins will come in much ore easily after a few usages. Some light sanding on the sides could make this break in go faster. Even a bit of silocone spray could hell. Or wait - a light rub with a good old (hard) piece of soap. And thn just take some care to put them in "straight" ie not with the front of back first. If the fins really go too deep in the box, let us know. But all my boxes have the right depth. The fins at most make a small little mark in the paint when mounted.
Let us know how things proceed.