Cash counting machines in banks scan and record numbers to find bills that have already been flagged (such as those stolen from banks/ATMs), but that process is unrelated to the crediting of money to your account. General cash tracking is hypothetically possible, but it would not be trivial to implement.
Well not _you_ but bills do get flagged if they're involved in crimes (like kidnapping or robbery). So when they're deposited in a bank the FBI can track the _relative_ location of criminals.