Continuity mistake: In the beginning, where it is showing how the Wonka chocolate bars are made, we see trays holding twelve pieces of chocolate. When it shows the trays on the conveyor belt, each tray holds fourteen pieces of chocolate.
Continuity mistake: In the scene when Agustus Gloop gets sucked into the chocolate tube, the inside of the tube is covered in chocolate. But in the far away shot, when you see the tube being retracted, it is perfectly clean inside and out.
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.