The charge sheet against Simatovic and Stanisic includes several paragraphs detailing the murders of thousands of Muslim prisoners from the town of Srebrenica in July 1995 and subsequent efforts to cover up the atrocity.
The judges wanted prosecutors to make it clear that as far as these crimes go, Simatovic and Stanisic are only charged on the basis of the alleged murders of six particular prisoners from Srebrenica, whose executions were captured in a home video which was made public last year.
Those seen in the footage carrying out the murders were allegedly members of a paramilitary unit known as the Scorpions, which prosecutors say was subordinated to the DB at the time.
The judges emphasised that any alleged links between this particular crime and a so-called joint criminal enterprise, including the massacre of thousands of other prisoners from Srebrenica, was "a matter for trial".
They also asked prosecutors to make it clear that Simatovic and Stanisic were not charged with deporting or forcibly transferring people from Srebrenica.