This whole thing is making the FBI look like a bunch of clowns...
I know a few people who have worked with them (not naming names), and they all agree that the FBI are nowhere near as slick as the media makes them out to be.
Yes, this is the source of their current troubles: being told to hold on to the evidence from that case.
EDIT: in -> from
Well, the files that they were told to hold on to were a majority of the claimed files (something like 35/37, IIRC) when the DoJ went after him.
But if you get a subpoena, you have no choice in the matter. I don't know the facts in this Megaupload/Ninja Video case, but this is hardly the revelation that Wired wants (?) to make it.