Nick Ansell was given his marching orders by referee Strebre Delovski on the stroke of half-time after he was adjudged to have tugged on the shirt of David Williams when the Heart attacker was through on goal.
The Victory were two goals down at the time thanks to strikes from Orlando Engelaar and a cross-come-shot from Mate Dugandzic, with Muscat conceding their already improbable task became impossible from there.
"I don't want to sit here and sound like I'm whinging because to be honest we made it as hard for ourselves as we possibly could with the two goals we conceded…but then to have someone sent off for something like that…" Muscat said after the game.
"It'll be justified as well by some letter of the law or whatever they want to sit behind but if that's denying a clear goal scoring opportunity when Lawrence Thomas has got the ball, it’s beyond me.
"Like I said that's not the reason we lost the game but that contributed to a poor game in the end."
The derby was the Victory's third game in eight days, with the side travelling to China following their win against Adelaide last weekend to face Guangzhou Everglade in the Asian Champions League, where they lost 4-2.
The hectic schedule appeared to have an effect on a lethargic Victory team, but Muscat was once again not making any excuses on his players' behalf.
'You can't tell me that travel and fatigue gifts opposition goals," Muscat said.
"It was the worst possible start we could've had considering the week we had. We give away a goal trying to play out and then the second goal, we give the ball away but it's an accident, it's a mis-kick.
"And then Stebre took over."
Victory have now conceded goals in their past five outings and with their defensive frailties once again exposed on Saturday night, Muscat admitted it is something his team must focus on going forward.
"I think the amount times I've suggested we give away sloppy goals and cheap goals, of course it’s a concern. If you're giving away goals, you're always asking yourself to do too much.
"Like I said, the week that we've had after that first 15 minutes it became very, very difficult, almost impossible. And then it was impossible after the letter of the law stepped in."
There were also questions over the selection of gloveman Thomas, who played in just his fifth game for the club, with Muscat insisting he had good reason to pick him ahead of Nathan Coe.
"Lawrence has been training well and I just thought it was an opportunity to give him a game. He's worked hard enough to get it (the opportunity to play)."
