I'm skeptical, too. How much active duty was he doing prior to applying for the position? How long since his previous urinalysis? How long did it take to get the initial report back? How long was his hair? How long does that drug stay in your system? All those would factor in to the believability of his story.
It is also pretty unlikely that samples were mixed up, or deliberately tampered with.
On the other hand, I definitely don't like the idea of using the results of a urine sample for this purpose unless you are going to have the "chain of custody" security.