Yes, there have been false positives from WADA labs, or cases where the A sample showed a positive and the B didn't. There are a few reasons this could happen
-the lab fucks up and reports a false positive. They detected something that wasn't there. This is rare, and labs have lost their accreditation over this before.
-the DCO or athlete fuck up, and contaminate one of the bottles during the sample taking process. This should be hard to do, and there's no reason someone would try. I'm not aware of any cases of a DCO fucking with an athlete due to corruption or anything like that.
-for some PEDs, the markers may deteriorate over time in the sample bottle, and so the A sample could show a (valid) positive, and the b show a (valid) negative, simply because molecules the lab was trying to detect weren't there anymore.
All cases are rare. If you gamble, placing a bet on the B sample matching the A is a safe bet, even at huge odds.