Has an AFL game ever ended 39-16?
Exactly once. On August 12, 1899, Fitzroy beat Carlton 39-16, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 39-16 in league history.
That makes 39-16 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 40-16 has happened never and 39-17 has happened never.