This expression is used by many to indicate that an exception in some way confirms a rule. Others say that the exception tests the rule. In its original legal sense, it meant that a rule could sometimes be inferred from an exemption or exception. In general use, the first meaning predominates nowadays, much to the annoyance of some pedants.
If something's a moot point, there's some disagreement about it: a debatable point.
In the U.S., this expression usually means that there is no point in debating something, because it just doesn't matter.
An example: If you are arguing over whether to go the beach or to the park, but you find out the car won't start and you can't go anywhere, then the destination is said to be a moot point.