Bristol Rovers are to lodge a complaint to the Football League and Football Association over an alleged breach of third-party ownership rules by Wycombe.
Last week, Wycombe were fined £10,000 for a breach of FA rules over the sale of Matt Phillips to Blackpool in 2010.
However, that charge was relating to breaking rules regarding agents and not third-party ownership.
The two sides finished level on points in League Two this season, with Rovers relegated on goal difference.
Wycombe were found guilty of agreeing to pay an agent through a future sell-on clause of winger Phillips.
The agent involved, Phil Smith, was banned for two years - 18 months of which was suspended.
Phillips joined Blackpool for £325,000 from Wycombe in 2010 and moved to QPR last year, which is when the offence came to light.
In a statement, Bristol Rovers said the infringement "led to Wycombe wrongfully obtaining a competitive advantage over Bristol Rovers".
It added: "Without this, Wycombe rather than Bristol Rovers could have been relegated."
A Wycombe statement said: "We will, as always, fully cooperate with the Football League and the Football Association in any investigation into this matter, but we are fully confident that there is no case to answer."