It is an offensive term meaning "What in the world have you done to my dog?" This is what Mrs Shears screamed at Christopher.
In this novel, the main character Christopher wanted to find out who killed Wellington, his neighbour Mrs Shear's dog. Mrs Shears thought that Christopher had killed it.
Like many people with Aspergers Syndrome, Christopher is obsessed with details, loves puzzles and gets confused by too much information coming at him. All of these elements come together as his quest changes from finding the killer of the next door neighbor’s dog to a quest of a much more personal nature.