I see no big problem with that first part at all. Seems like a honest accident - stuff like that can happen. No big deal, imho.
But investigating the returned board - not seeing the RMA sticker on it, mis-classifying the damage, not checking their own records on the board - and claiming it was "customer damage" without any hard evidence... and not ever double-checking anything at all, after the customer repeatedly insisted they didn't even open the box...
That's the real problem. It's almost impossibly sloppy to miss all that during any damage investigation, it's outright offensive to claim "customer damage" without having done any investigation to substantiate that claim, and it's complete madness, to spend a lot of time insisting on "customer damage" in discussions with the customer, without ever double-checking the board, the damage or the records.
That's the reason why it's hard to believe this was a honest accident. Because if it was a honest accident... how could they have never noticed their accident, while "investigating" and refusing a refund multiple times over? With an RMA-sticker right on the board, dated to before the date of sale?