Given the rampant corruption of Gallifrey, the guilty party could successfully manipulate the evidence so that a completely innocent scapegoat takes the fall. And even if the investigator found proof of the manipulation, their superiors would probably just shrug it off and say "but we've already prosecuted someone for the crime."
Isn’t that pretty much the plot, or elements thereof, for Deadly Asassin, Arc of Infinity, Trial of A Timelord, and The Infinity Doctor?