Specifically:
Originally posted by MTR 3.5:
Cards in different sleeves, tokens, and double-faced cards for which checklists are being used are ignored when determining deck (not sideboard) legality.
You are correct, this is TE - Deck Problem, Warning. Since the Head Judge eliminated the concern of Cheating, then this is the only infraction that matches the error. Unsleeved is different from any sleeves, but they were stored with the sideboard and thus can determine deck legality.
As for abusability, (a) that's why we investigate - which the HJ in this case did - and (b) it's rather difficult to sideboard in two cards that weren't sleeved, while taking two cards out of their sleeves, without being noticed. Not impossible, obviously - but it's just not a very likely method of Cheating.
Hopefully, the HJ also directed the player to find another way to store those cards!
d:^D