The League has discovered an error made in which they registered City players with Coventry City Football Club (Holdings) instead of within Coventry City Football Club Limited, where the Golden Share to play in the Football League lay.
It comes after the Sky Bet League One outfit, under hedge fund owners Sisu, in March placed CCFC Ltd into administration, with Holdings continuing to operate.
The Otium Entertainment Group - related to Sisu - successfully purchased the assets of CCFC Ltd but a Company Voluntary Agreement (CVA) could not be agreed with creditors ACL, which is the management company behind the Ricoh Arena, and the subsidiary is now currently facing liquidation.
As a result, at the start of August Coventry were hit with a 10-point deduction after the League transferred their Golden Share to Otium.
The knock-on effects of today's news of an administrative error, which is also understood to have been made by the Football Association, remains to be seen, but the League has already ensured a similar scenario, amid what is a complicated case, has not and will not be repeated at any other clubs.
But ACL, who had already requested that the FA intervene after Coventry's three-year groundshare with Northampton was given the green light, is again demanding that the case be taken to English football's governing body.
A statement released by ACL this evening read: "The Football League's admission that it has made serious errors in the administration of Coventry City Football Club is a crucial development in this saga.
"Since March, we have made the case that the football assets of the club, including player registrations, should have resided with the company with the 'Golden Share' - that is Coventry City Football Club Limited.
"That is what all the publicly available documentation makes clear - from the 2008 board minutes that recently came to light right through to the last set of filed accounts in 2012. It is also what the Football League's own regulations say should bethe case.
"It is therefore deeply disappointing that they have waited until now - with the administration process almost over - to make this admission. But fortunately there is still time to resolve this matter.
"The joint-administrators have not yet liquidated the club so there is still time for a proper administration process to be run - one based on all the facts - that provides a fair outcome for creditors, for prospective purchasers of the club, and most of all for Sky Blues fans themselves."
The Sky Blues and ACL, who run the Ricoh Arena on behalf of joint owners the Alan Edward Higgs Charity and Coventry City Council, have been involved in a lengthy and bitter rent row which has been ongoing for around 18 months.
Having left the Ricoh this summer, Coventry are planning to build a new stadium in the local area while they groundshare with Northampton at Sixfields for the next three years.
Coventry have since released their own statement, which reads: "As the club has consistently maintained, the players contracts have been registered by CCFC (Holdings) Ltd and registered by the Football League in the name of Holdings for over 10 years - way before Sisu took over the club.
"Today's admission by the Football League confirms that."
It added: "The mistake if there was one, was not that the players' contracts should have been registered in the name of CCFC Ltd, but that the Golden Share should have been registered in Holdings, which owned the beneficial interest in the club.
"We would now suggest the City Council and ACL drop their efforts to force a change of ownership of the club - conduct which is now subject to oral argument in the request for judicial review."