Usually when they test, they take two samples, an A sample and a B sample. This way if the A sample is positive, they can check out the B sample for a potential inconsistent result.
What we need to know, is if his B sample is what supposedly came up clean, or a subsequent second test at a later date. Usually the voluntary second test is a PR move, with the player knowing full well he is going to pass.
If it's the B sample, i'm not sure how MLB handles that. In MMA, the state athletic commission comes together and rules.