The breaches relate to the signing of Alejandro Faurlin, who allegedly was owned in part by a third party after moving to QPR.
Seven points clear at the top of the Championship, the club face a points penalty if found guilty and that could harm their hopes of promotion to the Premier League.
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Since Guus Hiddink arrived at the helm, Chelsea have improved considerably after a tricky start to the campaign.
Newcastle United are staring down the barrel of relegation to the Championship for the second time in the past eight years.