I've never had a problem with name matching even though all my tickets are issued with just my first and last name, but my FF cards do have a middle initial. My passport has first and last name only, but my NEXUS card has my middle name. Since the NEXUS card is never looked at, it has never been in conflict with my passport, even when it was issued. And AE has never kicked up a problem by my not using the middle initial on my AC or any other airline tickets/flights.
I do suppose it is a major issue if you alternately make use of a first or middle name and there is an inconsistency as a result.