as said, for competion, every shot out of the gun needs to be calculated into a group.
For determining a gun's accuracy, flyers can be taken into account. However, you have to truely be dealing with flyers. A flyer is a shot where you KNOW something went wrong, and can announce that fact before retreiving your target, and probably should be able to tell where on the paper the flyer will appear (went high and left because hot brass from the next lane went down my plumber's crack)
as said, the MOA accuracy of a gun is the size of groups it can produce 9 times out of 10. Just like a stopped clock is right two times a day, just random chance a gun will group shots closer together than the true accuracy of the gun on occasion. This does not work in the reverse, however, outside factors such as a change in breeze, barrel heating, shooter fatigue, etc can cause 'quasi-flyers' - shots that are a little off not due to the gun but due to the shooter.
I think the best method of determining how good of groups you or your gun can shoot is a trimmed mean. Shoot X shots 10 times, drop the best target and the worst target. measure the remaining 8 and average them.