Yep. It happens. We catch a lot of them, but some inevitably slip though.
Remember that your drug testing program is mostly about deterrence. We get a fair number of positives, but there would be a lot more drug use if there were no testing at all.
A number of safeguards in the collection process help prevent donors from substituting clean urine for their own. Bags and outer clothing are removed, pockets are checked, and the temperature of the urine specimen is checked.