With 85 players on scholarship, it's hard not to have duplicate numbers and maintain any semblance of positional number structure (though that hardly means anything today anyway with everybody kind of wearing every number).
In the NFL, the roster is limited to 52 players, so it's easier not to have that overlap.
The times I remember it coming up was:
During the Egg Bowl when Freeze was putting Nkemdiche in as running back wearing number 5. The refs made him change his jersey because Ole Miss already had a #5 running back so he wore #99 the rest of the game and didn't gain another yard.
During the Memphis game 2 years ago when the ball was downed and the ref put his hand up, but then allowed the Memphis player to return the punt, Memphis had two players on the field at the same time with the same number, but didn't get called for it.