Has an AFL game ever ended 45-41?
Exactly once. On May 7, 1960, Carlton beat St Kilda 45-41, and no AFL game before or since has ended that way. When it happened it was a scorigami, the first 45-41 in league history.
That makes 45-41 the 3836th most common final score out of 6,607 that have ever occurred in AFL. One point away, 46-41 has happened 2 times and 45-42 has happened 2 times.