Steve Clarke says referee Steven McLean had "no control of the game" as his Kilmarnock side lost 2-1 to Hearts.
The Rugby Park side missed a chance to narrow the gap on Scottish Premiership leaders Celtic as their seven-game unbeaten run ended.
Manager Clarke thought McLean had waited too long to issue bookings.
"If you leave all your yellow cards until later stages, you get a lot of breaks in the play towards the end of the game and it suits Hearts," he said.
- Hearts spoil Kilmarnock bid to narrow gap at top
- How did you rate the players?
- Sportsound podcast: 'Hearts just deserved it'
"If you see it is a physical contest from the start, you bring out a couple of yellow cards, it allows the more creative players to try to play.
"It probably worked against us later in the game when Hearts were allowed to make foul after foul to break the rhythm and determination of our guys to get forward."
Goals from Hearts' Sean Clare and Steven Naismith were followed by a Jordan Jones penalty in a seven-minute spell before the break and Clarke thought McLean should have ruled out the visitors's second.
"It was a foul for the free kick as well because Naismith blocks off Chris Burke, who is trying to cover the outside of the wall," he said.
"Fair play to Hearts. They were clever. You've got to give them credit for that, but if the referee's alive then maybe we don't get punished for it."
Clarke said of his side it was "a disappointing result, not performance - the performance was good" against a team intent on defending.
"Hearts came here obviously to make it difficult for us and sat in - five at the back, four in midfield - made it difficult for us to create too much," he said.
"It is difficult when you've got three big lumps defending the box very well. We will play a lot worse than that and get three points."