Cox was standing in for boss Neal Ardley at Prenton Park as the Dons chief recovers from hip surgery and oversaw a 1-1 draw for the visitors.
Bayo Akinfenwa’s opener was cancelled out in stoppage time by on-loan Everton youngster George Green to leave Wimbledon seven points off the play-offs.
If that wasn’t tough enough to take for the Dons, the away dugout was up in arms over referee Andy Woolmer’s decision not to award a penalty for a challenge on Ade Azeez.
Cox made his thoughts known post-match and joked it was probably best that the absent Ardley wasn’t able to give the officials a piece of his mind.
He said: “It’s a good job I’m here and he isn’t going in to see the referee.
“It was a definite penalty. I think that’s the fifth or sixth time we’ve an opportunity for a penalty turned down.
“Obviously I’ve got to be careful about what I say because I don’t want to have a go at the referee but he’s in the perfect position.”