I'd say the cause is uphauling and the recessed mast track/higher rail. When standing on the board with the rig in the water because of the higher rail the mast is going to be resting on the deck at 1 point, which is where the dents look to be. Is your mastpad on the sail long enough to cover the mast at that point? The board is 80cm wide. The board is a light construction for freerace which is fair enough. When slalom/freerace boards came out with recessed decks it put me off them, as I had seen a few with dents there. Speaking to a slalom sailor, he said that in between heats he sometimes sits on the board with the rig in the water, rig sunk a bit. To help uphaul they sometimes stand on the rail to help lever the rig out of the water! The use larger sails than you (I guess you dont use 8.5m+) but I think it could still cause damage.
I would say boards which are uphauled a lot (beginner boards) dont have the recessed decks and dont think foil boards have recessed decks either. (Wow that lowered centre of gravity really does help control massively for the freeracer/freerider

, not.)
I was going to buy a Bolt 125 when they came out, but stalled when I saw they had the recessed deck, earlier smaller Bolts hadn't. I nearly changed my mind but a decent older board came up secondhand.
If you can hear crunching when you press it, it is the carbon flexing, so needs fixing.