I had some involvement with a similar case when I was working for an airline many years ago.

In this particular case the travel agent had charged a fare that was valid for the trip - but not being able to get seats in the right fare bucket for every leg of the flight they had booked some sectors in a higher booking class - i.e., these passengers were travelling on a fare corresponding to something like a V (=cheap Economy) booking class but were booked in something like S (=expensive Economy). The discrepancy got spotted by airline staff, and the travel agent ended up having to pay the difference between the fare they had charged and the fare they should have charged.

I wonder if something similar happened here?

Another point - the OP states the tickets were issued by Austrian. Tickets booked through appointed travel agents are usually issued by the travel agent, not by the airline - they may look like they were issued by the airline because the have the airline's name on them and are printed on the airline's ticket stock, but it's usually the agent, not the airline, that does the ticketing... so the first time any Austrian Airlines staff would have seen this ticket would have been at check-in.

BTW, I take it this Skytours outfit is www.skytours.at?