The ending "-tion" is a common suffix in English, derived from the Latin "-tio," which is used to form nouns from verbs. It signifies the process of doing something or the result of an action.
The ending "-sion" is also derived from Latin, but it is used to form nouns from verbs that have a different stem than the Latin "-tio" verbs. For example, "permission" comes from the Latin "permissio."
So, because "question" is derived from the Latin "quaestio" which uses the "-tio" stem, it is spelled with "-tion."