The only time I've had this kind of problem was with SQ! In Feb this year, I was booked LHR~SYD, via SIN (straight through with a just couple of hours layover, longer than planned due to a mistake by SQ). When I tried to check-in online, I was refused. Spoke to their helpdesk and was told that my passport would expire in less than six months and they could not accept that and I could not travel.
This started a long series of enquires over the next 24 hours and included me pointing out to SQ that, I had given them my passport details months before when booking. Their reply (on the phone and at the airport) was:
We have to ensure that all our passengers comply with the requirements of the destination country.
I said (many times): "I have done, and Australia have issued my E-visa and here is the detail printed out. If Australia had not accepted my soon to expire passport, I would have replaced it in the last three months."
"But we cannot let you board as you might want to leave the airport in Singapore."
"I have no intention of the leaving the airport in Singapore."
Repeat as required ...
The previous evening, I had read the detailed Ts&Cs of the ticket and there was no reference to the rules in SIN, only the destination country.
Eventually, at the aiport, they produced a form which they filled in. It was headed 'Irregularity of Travel Document', which kind of gave the game away that they had done this to their pax before! I got the impression that the senior agent who had been summoned knew the stupidity of this but he did what he had to do.
We filled it in and I promised to indemnify SQ against all sort of ghouls and goblins (I still have my copy of it) and away we went.
In all other regards, SQ were brilliant. But I have seen more examples where carriers and countries now reckon a 5 year passport is only valid for 4.5 years.