Definitely contact customer service. He deserves the IDB compensation (cash, not vouchers of any sort), PLUS IMHO additional compensation for the way they munged the situation.

As for how that happens, I don't know... but I saw a full flight ABQ-DEN with several standby pax who'd cleared end up with at least 5-6 double seat assignments. I think they were able to accommodate everyone, but none of the FAs could figure out what the deal was. I think one problem was that the GA had let some standbys board with their original flight's BPs and forgot to give them their new ones, but that didn't account for all of the double assignees.