Abafana Bes’thende advanced to the quarterfinals having scored the decisive goal moments after referee Michael Mosemeng failed to award Stellenbosch what appeared to be a clear spot kick for a handball inside the box.
Speaking after the match, Mngqithi acknowledged it was becoming increasingly evident that referees were struggling to keep pace with the modern game.
"The speed of the game is fast so you need technology to make decisions. The speed of the game will always be faster than the referees, and sometimes the referees are forced to make conclusions, but when you have a second chance to look at it, you will be able to see exactly what happened.
"I would appreciate to win a match without such issues, because I've been talking about this all along."
While it was Stellies who felt hard done by on Saturday night, Mngqithi argued their rivals have also been on the receiving end of some costly decisions.
In his overall reaction to their narrow win, the Arrows coach pointed out they were not at their best on the night.
"We were a little bit timid in the midfield today. Two of my midfielders were not at the level we expected and that made us struggle with our build-ups. Fortunately, Stellenbosch did not punish us from those set pieces in the first half. It was not a very good start from us, but we came back stronger in the second half."
Mngqithi is hoping a KZN team can go all the way in the cup with AmaZulu also through to the last eight of the competition, albeit at the expense of their neighbours Richards Bay on Friday night.