Other mistake: Squirrels are used in the factory to get nuts out of shells. Mr Wonka states that they tap the nut first to make sure it isn't a bad nut. However, this is never done until the action is pointed out.
Continuity mistake: The jacket that Violet wears has a zip. However, this zip disappears without trace once she is a blueberry, and remains missing for the rest of her existance as a blueberry. Violet's body was done in CG animation, so it could not be that Violet had to change into a different costume. There was no reason why the zip couldn't remain, it just seems like the CG makers got tired of it being there.
Answer: We are never shown what happened to him but he may have gone to live with relatives or he was simply put into an orphanage.