It's all because of change left in the machine by previous people dumping, whether in the reject tray, the chute leading to the tray, or in the actual machine itself.
It definitely pays to know how much you're dumping into the machine. When I get shorted, I'll pull out the metal hopper thing and 98% of the time I'll see coins of mine that didn't get counted for whatever reason. I'll just hit "GO" again and run the machine and print another ticket out. For the other 2%, it is coins that got rejected.
People who are just dumping random change most likely haven't counted it out, so they don't know if they are getting shorted or not. Which obviously benefits me.