The Owls, their owner Dejphon Chansriri, finance director John Redgate and former chief executive Katrien Meire have been charged with misconduct over the deal which saw Hillsborough sold to one of Chansiri's companies, and leased back.
Clubs are permitted to do this as a way of getting around the Football League's profit and sustainability rules, and Derby County, Aston Villa (when in the Championship) and Reading have acted similarly.
In Wednesday's case, it allowed them to avoid breaching the rules which limit losses to £39m over a three-year period.
The issue appears to be not the fact that Wednesday did the deal, but the mechanics and the timescale of it.
The Owls are bemused and frustrated because they communicated with the League throughout the process, but are now saying they are blocking the Owls' claim and refusing to engage.
The Football League have handed the matter over to an independent disciplinary commission, as per their rules.
“The club has issued its claim against the EFL for acting unlawfully in relation to its alleged disciplinary charges,” read an Owls statement.
“We have sought to engage with the EFL in order to agree a sensible procedure to resolve the dispute arising from the fact that the club relied upon representations from the EFL in relation to the sale transaction which is the subject of the charges.
“The club regrets that the EFL has so far refused to agree to the club being permitted to make its claim, and refused to agree to a sensible procedure for dealing with the dispute.
“The club will continue to take such steps as it considers necessary to protect and enforce its rights against the EFL and to protect it from unlawful action by the EFL affecting the club and the performance of its team.”
A points deduction of up to 21 points has been mooted as a possible punishment for the offence, which would be the first of its kind.
Last season Birmingham City were deducted nine points for breaking the profit and sustainability rules – the Football League's equivalent of financial fair play. Wednesday have not been charged with breaking these rules, but with misconduct.
Grounds are supposed to be sold at market value, and there have been eyebrows raised at the £60m price Chansiri's company paid for Hillsborough, Wednesday's home since 1899.
That allowed a pre-tax loss of £35m for 2017-18 to become a £2.5m profit, yet according to Land Registry documents the sale was not completed until the following financial year. The money is due in seven instalments over eight years.
When the charges were laid last month an EFL spokesperson said that, “following the review of a large number of documents provided by the club - some of those seen for the first time - evidence came to light to justify the multiple charges of misconduct."
The Owls say they have prove that the League sanctioned the sale.
Garry Monk's team are in the Championship's play-off places by a point from Bristol City, their visitors on Sunday. Nottingham Forest are a point further back with a game in hand. Wednesday are 18 above the relegation zone.