At the end we see a soldier replacing the canister that the Zyklon B is kept in. However, he is not wearing an SS badge as all SS soldiers did. Zyklon B was only handled by members of the SS, as no other unit had authorisation to carry the sensitive stuff.
In the scenes inside the camp, the boys were both meant to be barefoot. However the actor who played Bruno's parents vetoed it, and thus the boys were allowed to wear shoes.