In Canada, after you fill out your ballot in secret, you fold it up and hand it to the poll worker, who tears off a stub and then hands the ballot back to you, and then you insert it into the ballot box yourself in plain view.

I don't know if this is the current case (or perhaps your scenario is one of the reasons for the current procedure), but they can just put a serial number on the stub so that the poll worker can verify that the ballot that was handed out was the one just filled out.