Sundowns were knocked out at the semi-final stages after losing 3-1 to to the Team of Choice, who rallied from a goal down to dispatch the PSL leaders.
And Mosimane feels the need to bring off Ngcongca due to injury 10 minutes into the second-half severely disrupted his side's game plan.
“Mekoa is on a second yellow card and kicks Anele off the pitch. We lose Anele, Mekoa receives a talk. Gaston is on a yellow and gets dismissed," Mosimane told SuperSport TV.
“I’m not saying it shouldn’t have been because it was a foul but I think the ref didn’t manage the game well. We tried to equalize but they set back. We controlled the game in the first half.
Mosimane felt his charges had enough chances to finish off Maritzburg after taking the lead.
“I think we scored early and had the chance to score the second from a number of chances. Vila scuffed the ball in front of goa, we should’ve finished with Percy as well. We should’ve finished the game there but we did not.
“I think the equaliser was a brilliant goal. We didn’t overload the throw-in, allowing it to go on the other side but their inter-passing was brilliantly done. It was a brilliant goal no doubt about it,” he added.