The Rams are going through a tough phase with an enhanced transfer embargo due to a breach of regulations.
They have just nine senior players registered and now look set to be without Knight for a while.
The club recently stayed at Pennyhill park for their pre-season camp, where Rooney took part in training due to the lack of players.
It is now reported that Knight was on the wrong end of a Rooney challenge that could rule him out for 12 weeks.
Rooney was appointed as the permanent head coach during the back end of the previous campaign.
Although the club made a positive start, their form was poor in the final months, as they just avoided relegation.
They are now under a transfer ban, although the English Football League are likely to permit them to sign up to five players that are free agents or available on six-month loan deals.
Curtis Davies and Andre Wisdom appear likely to sign new one-year contracts after their previous deals expired on June 30.
Manchester United graduate Ravel Morrison has been on trial in pre-season and could also be handed a 12-month deal.
Stats from Transfermarkt.com