There are no good guys here..
Watching Clen-gate unfold I can't help but feel a certain deja vu with the Flandis Affair. I have a lot of very specific thoughts on the situation, none of which fit well into a short blog post and I am tempted to do a Nate Silver live 5-part series.
The bottom line for me is that, while Contador is likely guilty of doping, it does not appear that the test he failed is evidence of this. Rather, there seems to be a reasonable chance that trace amounts of Clen can occur in a persons system through environmental contamination. Without studies that identify the risk from food contamination we don't know what the effective false positive rate (defined here to include both positives where no Clen is present and positives where the athelete did not intentionally ingest the drug) is nor do athletes know where the contamination may be coming from. While it is the athletes responsibility to know what goes in there body it does not seem that an athlete can reasonable avoid consuming food that may be contaminated.
I have to repeat, none of this is to say that Contador is innocent. I think the point is that the test itself appears to be inconclusive and doesn't really add any additional evidence beyond our own certainty that all athletes (except those from your home country of course!) dope. And it's always dangerous to decide someone is guilty just because we "know" he is and then look for confirming evidence with an uncritical eye because.. well.. turns out human certainty isn't really all the reliable.