Well that has happened to me once or twice but 'anytime after 36 minutes' sounds more like a problem setting a lineup.
Nope, just checked. 9 players, everyone assigned to a position. Player assigned to all three positions. The only change was that I used "According to Depth Chart" rather than "Strictly According to Depth Chart" which should still be ok, if I understand the rules correctly.
It's probably some specific combination of settings.