The Jets fell 2-1 to a second-string Brisbane Roar on Friday night at Suncorp Stadium, a result that seals their fate as the competition's bottom-placed team this season.
The loss came hours after Tinkler was cited under FFA's national code of conduct for a reported 15-minute verbal tirade directed at Newcastle Herald journalist Robert Dillon.
Stubbins, who has enjoyed the chairman's firm support throughout an abysmal A-League campaign, attempted to sidestep questions regarding Tinkler's alleged outburst.
"They're comments that's allegedly been made by the owner," Stubbins said.
"I don't really want to comment on that, but that's what's been put to print, so we ride that one.
"It's always disappointing if you have to bear that but I don't want to go into anything surrounding that."
Asked if it may have affected the players, Stubbins said: "We're not using any excuses, so well leave that one alone."
According to Fairfax Media, Tinkler is alleged to have spotted Dillon after last week's 4-3 loss to Sydney FC and then unleashed a torrent of abuse at Dillon that not even an intervening Jets official could stop.
Tinkler allegedly described Dillon and the newspaper as a "cancer" and accused him of "spreading cancer" before declaring: "I hope you get cancer and die."
Dillon last year won a Walkley award for his coverage of the collapse of Tinkler's sporting empire.
Tinkler has until next Friday to explain why he should not be sanctioned by FFA.
Meanwhile, Stubbins has vowed that the Jets will be in a better position this time next year.
Nine players are coming off contract, giving Stubbins the scope to completely revamp Newcastle's playing list.
Tinkler has already promised to fund two marquee players, an Australian and an international.
"Where to from here is up," he said.
"We know where we are, it's been a disappointing campaign.
"There's been a hell of a lot learned this year, that's for sure.
"We've done very well against teams that have been at the top end on occasion but we just haven't done it often enough.
"It's well documented now that we've got a lot of opportunity to bring in fresh blood. We'll do that."