The hosts gave up the lead twice to lose 3-2 at AAMI Park on Sunday, missing a chance to replace Perth Glory at the top of the table.
Asked if the sting of failure was being felt more keenly on what was meant to be a landmark day for the club's veteran forward, Muscat was unequivocal.
"Without doubt," he said.
"In football, you've got to remove emotion from everything you do. But I'd be lying if I said we weren't really disappointed not to commemorate his 200th with a win."
Victory's defence will be come under heavy scrutiny for the manner of the goals they conceded, but Muscat insisted the whole team were at fault for failing to open up a decisive advantage during a dominant performance in the opening 45 minutes.
"If we look back at that first half, we had enough clear-cut chances to be a few goals ahead," he said.
"To concede like we have done from set-pieces is criminal. We shoot ourselves in the foot.
"We've got to defend set-pieces better. But we can't just point the finger (at the defence).
"There was a number of other things we could have done better."
The Victory boss also brushed aside any suggestions Wellington's winning goal should not have been allowed, after Nathan Burns moved from a passive offside position to become active and decide the contest.
"When the ball's played to him he's clearly onside," he said.
Matthieu Delpierre made his first appearance since October after recovering from a long-standing foot problem, with the French centre-back potentially the answer to some of Victory's defensive frailties.
"Another week under his belt," Muscat said.
"He's been making steady progress."
The veteran could yet start when Victory host Glory in what is shaping as a huge crunch match at the same venue on Saturday night.