If this is a cover story (which I highly doubt), I'd say it's a pretty creative one. I'm assuming the Brewers will bring him back at the end of the suspension.
Somewhat-relevant anecdote -- a few years ago I ran a race that had a randomized drug testing policy using the extremely long list of drugs prohibited by the world anti-doping agency. Good luck running your prescriptions/supplements against that list. I'm assuming that many of these minor league guys do the same thing that I did -- plug whatever they are taking into Google and figure out if it's likely to cause a positive test or not. If you do that for Clomid, you do get some results suggesting it could cause a positive test. So, yes, this is on Pedro for not doing his due diligence, which he has admitted and apologized for. That's life.