The way I interpreted it, is that he is warning there may be conflicting orders delivered and they want the troops to follow the unified command, which would be a series of agencies working together, according to a web search. I think Pence has a role to play in all of this and his role may have been the fall guy to ensure the cabal went through with their plan. As Trump said when speaking about Pence during his speech on the 6th, sometimes it takes bravery to do nothing.