Has an AFL game ever ended 99-90?
Yes. AFL has seen a final score of 99-90 6 times. It first happened on June 1, 1946, when Footscray beat Hawthorn, and most recently on August 25, 2017, when Hawthorn beat Footscray.
That makes 99-90 the 342nd most common final score out of 6,607 that have ever occurred in AFL. One point away, 100-90 has happened 5 times and 99-91 has happened 4 times. At one point the score disappeared for 37 years, between 1946 and 1983.