Had a similar issue booking tickets for myself and a couple of friends. Friends have a three-part surname - they only go by the last two, but the full monty was given in passports and wouldn't fit into the airline booking system. Rang said airline to query, and was told to use the last two only.
We checked in OK but were called back to the desk five minutes later. There followed a bit of scowling from security bods, examination of passport photos against faces by half a dozen different people, and all was OK.
If we managed to get by on the omission of a third of a surname, I'm sure an odd apostrophe won't be an issue.