Several theories about about how Contador (AC) may have ended up with the trace amount of clenbuterol in his blood. One possible theory being explored is that AC was using clenbuterol weeks before the Tour de France and thought it had cleared his system when he then gave blood for future blood doping. Then, on the rest day, he transfused his blood (with the trace amount of clenbuterol) and the clenbuterol showed up the next day in his urine.
Some experts are alleging that those who transfuse blood have higher amounts of plastic residues from the blood transfusion bags and reports are going around that AC showed a high concentration of plastic in addition to clenbuterol. (Interestingly, one reader pointed out to me that this may be what happened to Floyd when he ended up with excess testosterone in his blood. It's possible that the reason he is still claiming he didn't take testosterone the night before he failed the test is that he transfused his blood from a prior period and the blood had excess testosterone in it.)
Apparently, the UCI has another theory that allows Contador to keep the yellow jersey and for pro cycling to save some face. To have another Tour de France winner lose his yellow jersey would be bad for business and would reflect poorly on the UCI. As for the UCI's theory, Contador gave the following account: