Craig Dawson's goal put the home side ahead only for late strikers from Michael Flynn and Scott Neilson to win it for the Bantams.
Hill said: "I'm really disappointed with the result but I'm more disappointed with the referee's performance - it was just not acceptable for this level.
"I felt he should have given Chris Dagnall a free-kick on the edge of the Bradford box but he didn't, then he contrived to give them two free-kicks on the edge of our box which, for me, were probably not free-kicks.
"We should have defended the free-kick that led to their goal better but at the end of the day the free-kick came about as a product of him not giving us a free-kick. His refereeing standard was not acceptable for a Football League match."