I think this question depends a lot on what you consider Candide's "crime" to be. He has done several sketchy things in the book so far, like killing three people, some in self-defense and some as preventative measures, but I think his over arching "crime," especially according to Voltaire, would be his insistence on his protagonist views. He has been a firm believer in Liebniz/Pangloss' philosophy, his faith wavering at times but never failing to return to him.
In this sense of a crime, I think his punishments do fit it. Voltaire is playing with him, as a test subject to test the validity of the idea that all is good in the world. He keeps throwing him all of these terrible, unexplainable things to show him that it is not so easy to explain everything away with the sweeping statement that all is for the best. When Candide insists on holding his beliefs, Voltaire punishes him by showing how harsh his ideas can be by testing him with the pain and suffering of someone he loves, Lady Cunègonde. He is trying to show to the reader and to Candide how the philosophy gets harder and harder to stand by when terrible things happen for, seemingly, no reason at all. Every time Candide has been "punished" he has doubted his beliefs for a moment, and then something else has happened that solidified them in his mind and let him return, in full, to Pangloss' philosophy. Voltaire's world then responds by punishing him again, trying again and again to show Candide how wrong he is and what a harsh place the world can be.