Hello.
I am relaying this but I believe I have the full story. I am wondering what really happened and what should we do.
-Purchased two economy tickets DL issued BOS-X/CDG-AGP and AGP-X/AMS-BOS.
-Economy class V outbound Q return on 006 stock. Outbound operated by AF on both segments. Return DL coded TV operated AGP-AMS then DL coded KL operated AMS-BOS.
-Passengers get to check in desk manned by Aviapartners at AGP. Told they owe $320 and have to return to Transavia ticketing desk (manned by Aviapartners staff).
-Staff there tells them they get a list of DL coded passengers who owe money each day but they don't know why and can't accept payment. They expect passenger to call DL and correct.
-Passengers call Delta who tell them to call agency.
-Passengers call agency who verify e-ticket matches itinerary. There was never a modification to the itinerary where an additional collection wasn't collected or a schedule change or anything like that.
-Agency calls Delta Agency Global Support. They are just as shocked as agency and verify with their ticketing department nothing is wrong with the PNR.
-Delta Agency Global Support relays through passenger, who is on phone with agent, to have Transavia desk put message/OSI in the system explaining they are denying them boarding.
-Transavia (Aviapartner staff) advise they can't put notes in record.
-Passenger, on advice of agent, tries only real Skyteam ticket desk at Malaga (Air Europa) without success.
-Delta apologizes to agent but advises without notes in the PNR, at this time, they have to view this as a voluntary change and collect fare difference to get them home on a different flight as the original departure has taken off while all this was going on.
-DL Global Support Agent and her ticketing staff are surprised, as is experienced and trusted agent, who can't figure out what has happened.
-Passenger has to pay $140 per person to fly KLM AGP-AMS that same afternoon, overnight for $500 at Sheraton Schipol and home the next morning on DL AMS-BOS.
-DL said save all receipts and deal with DL Customer Service upon return.

Can anyone guess what occurred?
A weird IT issue?
Again both the senior/experienced travel agent, DL Global Support for Agents and DL ticketing could find no reason why the PNR should not have been able to be checked into.
Thanks for advice and comments.