Referee Anthony Backhouse pointed to the spot in the second minute of stoppage time when Joe Edwards pushed Tommy Conway in the back in the penalty area.
The contact was fairly minimal, but Backhouse still deemed the offence to be worthy of a both a penalty and a straight red card for the Plymouth skipper.
Boro felt they should have had an earlier penalty when Julio Pleguezuelo appeared to catch Morgan Whittaker with a trailing leg, but on that occasion, Backhouse waved play on.
Muslic was hugely disappointed by the decision to award Boro a spot-kick in stoppage time, and felt Backhouse was influenced by the home side’s attempts to win previous penalties.
He said: “We got Middlesbrough frustrated, and they were asking four or five times for a penalty.
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“I don’t think you can react as a referee to that. Even if they fall to the ground ten times, if it is not a penalty, it is not a penalty.
“But to come up with such a big decision, and give a straight red card to Joe (Edwards), it is really tough.
“We can’t take it back. There is no VAR around to check. I think the lads played a brilliant game. Everything we prepared before we actually delivered and we did it. We knew the quality of Middlesbrough.
“Very strong in possession, very strong offensively, capable to break the lines easily. Very, very tight and players always inside the pockets.
“We did it actually very well and kept consistently our transition threat. Creating so many goal scoring opportunities. I think we had today five or six big, big ones. Shows just the strong performance we have or we had.
“And then losing this game or losing this very much deserved point with a 94 minute penalty. Yeah, it hurts.”
