Cooper was quoted by The World Game as saying Saturday's AFC Champions League playoff in Geelong would be his last match in charge, with his agent also claiming this week the coach had resigned from the Thai club little more than a month after joining.
The Englishman has since denied making the comments, attributing them to 'a trick from the Australian side clearly meant to unsettle the team'.
When asked if Victory had any involvement in attempting to unsettle Cooper and Muangthong, Muscat said: "None what so ever. It's actually insulting to be honest. It's got nothing to do with us, it's someone else's issues.
"It doesn't interest me. We've got our own focuses and our job to do. Someone else's issues is certainly the furthest thing from my mind."
Regardless of the source of the reports or the reason behind them, Muscat does not believe either side will gain an advantage on the pitch as a consequence.
"It's a one-off playoff," he said.
"If there wasn't this turbulence, what? Were they going to try a little bit less? I don't really understand it to be honest. The reality is both teams tomorrow night, regardless of anything that's happened in the last 24 hours, will have been trying their utmost to get a result.
"We'll be up for the game tomorrow night and we want to qualify for the Champions League."
Victory's regular homes, AAMI Park and Etihad Stadium, were both unavailable for the ACL playoff, meaning the all-important fixture will be staged in the unfamiliar surrounds of Geelong's Simonds Stadium.
But Muscat does expect his team to be disadvantaged by playing at the Australian Football League venue.
"It doesn't matter. We're here tomorrow night and I'm actually happy we're in Geelong," he said.
"We've played a game here previously, we've got thousands of fans that travel down from Geelong to watch us play in Melbourne whenever we're at home.
"So from our perspective we'll return the favour, come up the road and perform here in Geelong. And I've no doubt we'll get well supported, I'm looking forward to it."