Batley Bulldogs have been charged with fielding an ineligible player in their win over Sheffield Eagles last month.
Doncaster will face a similar charge of breaching competition rules on dual registration players in the same round of Championship games.
The clubs will face an independent tribunal next Thursday and if found guilty could be fined and/or have points deducted.
The claims centre on the controversial dual registration system where players signed to Super League clubs are allowed to play for Championship clubs.
It is alleged that Batley and Doncaster both fielded players, with a salary cap valuation of more than £20,000, who had not previously appeared in three games for the Championship club, after the dual registration deadline.
Huddersfield Giants’ forward Jacob Fairbank scored the final try for Batley in their 28-18 win at Owlerton. The Dons had Hull FC centre Ben Crooks in their team in their defeat at Keighley.
Both matches were played on Sunday July 27, two days after the registration deadline for the Kingstone Press Championship closed.
Dewsbury Rams have been cleared of an allegation that they fielded an ineligible player in a Championship fixture against Barrow Raiders on the same day.
The charges will be heard by an independent Operational Rules Tribunal which has been scheduled for Thursday August 14.
Any decision to deduct points could affect the final league placing with Eagles and Batley chasing a play-off place and separated by only one point.