Despite winning the matches on the park 3-0 defeats have been awarded with both clubs warned about their future conduct.
Development League matches are of little relevance with clubs using the fixtures to give players match practise and stay sharp.
On December 19 Raith fielded a trialist without the correct paperwork in a 1-1 draw with Stirling Albion.
Earlier in the month Queens Park were guilty of a similar offence when they beat Stranraer 2-1 but that result has now been reversed.
Andrew Dickson was in charge of player registrations and is now a member of the Scottish FA Football Regulatory Advisory Group.