According to this ESPN article:
The sample was in a tupperware container and sat on the collector's desk for the entire weekend. Turns out there were 12 FedEx locations open at the time, so it sounds like the collector royally screwed the pooch on this one.
I think he was taking something. I also think that the sloppy chain of possession opened the door to reasonable doubt (to use a court term).
Apparently the collective bargaining agreement is very anal about how these samples are to be collected and tested, so it is up to the collection agency to meet those standards. If they fail to do so, the MLB should not be surprised when the system lets a player off the hook.