The Owls' inability to meet their responsibilities has been a feature throughout the pandemic, with players not receiving all the money due to them on numerous occasions throughout the Covid-19 pandemic.
The most recent episode is understood to have been settled, but the Football League have stepped in to try to stop it happening once again.
There are reports that at least two, unnamed contracted players served notice on the club that they would leave if the money owed was not paid to them, as the rules allow. They and their team-mates have since got that.
Wednesday, who were deducted six points in last season's Championship for an unrelated pre-Covid financial fair play (FFP) breach around the sale and lease-back of Hillsborough to owner Dejphon Chansiri have been told they will be docked six more if there is a repeat in the first half of the season. A failure before June 30 will see a three-point penalty.
Last season's points deduction caused the Owls to be relegated to League One.
Derby County who have also been punished for breaking FFP rules over the sale of their ground, have also accepted a suspended deduction if they fail to pay wages fully, in their case three points.
With Derby's FFP punishment still being contested, the Rams escaped Championship relegation at Wednesday's expense on the final day of last season.
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