Saturday night's 1-1 draw at Etihad Stadium has left last year's grand finalists stranded in eighth place - one ahead of Brisbane - with four draws and two losses.
Victory have never had such a poor start to a season and can ill-afford to go winless for much longer if they are to avoid missing the finals for the first time since 2011-2012.
Their cause hasn't been helped by the absence of Socceroos duo James Troisi and Mark Milligan and New Zealand representative Kosta Barbarouses on international duties.
Troisi and Milligan will line up in Sydney on Wednesday night for the second leg of the Socceroos' 2018 FIFA World Cup qualifying play-off against Honduras.
Barbarouses, meanwhile, faces a gruelling trip to Peru for New Zealand's return leg and won't return to Australia until Friday.
Muscat said it was too early to tell whether they would be available for Victory's trip to Perth to face the fifth-placed Glory next Sunday night.
"It's dangerous just to assume things are going to turn around," Muscat said.
"Millsy and James have got a game on Wednesday night, Kosta doesn't arrive back until Friday and we've got a game on Sunday.
"I don't think we're out of the woods in terms of getting everyone back."
Muscat's men looked to have done enough against Brisbane when Besart Berisha scored in his return from suspension in the 79th minute.
But Roar drew level minutes later when substitute Brett Holman managed to get on the end of a sweet Jack Hingert cross and nail a straightforward finish.
While new additions Leroy George and Rhys Williams continued to impress, Muscat was left deeply disappointed by his side's inability to hold onto their deserved lead.
"You take four or five players out of any team in the league and I daresay it'll be difficult for them," he said.
"That's why if anything I was gutted for the group because the mainstay of that group that have been there every game of this season have worked so hard under a certain set of circumstances.
"Three points tonight would have rewarded them and unfortunately it didn't occur for us."