That seems unlikely. When a company wants to issue new stock, it informs the TA, who does the actual issuances and records them. So the TA and the company should be on the same page at all times.
There've been cases in the past in which management has had a block of certs it handed out to people without letting the TA know. But that's just asking for trouble, and even most of the sleaziest penny CEOs wouldn't dream of trying it.