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.

They actually do.

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.