Are you transfecting plasmids for you virus production? 

Yes, viral plasmids were transfected into HEK-293 cells 

If you have transfected a transfer plasmid (WPRE) in your mock wells, you could have carry over DNA (DNA that was not removed from your RNA isolation) in your qPCR reaction that results in a false positive. 

To begin, you might want to consider the possibility of RNA contamination in your qPCR master mixes/reagent stocks. If testing/replacing those does not solve the problem, work backwards doing the same for earlier steps (reverse transcription, RNA extraction, etc.)