No, it doesn't; the petitio principii fallacy sense is inherently intransitive in structure (with no direct object), the “raises the question” sense is necessarily transitive (has a direct object, specifically, the question raised). They are unambiguous (and the intransitive sense cam be rationalized as a special case of the transitibe sense where the unstated object is the justification for the original claim, which is convenient since otherwise that sense is completely opaque in terms of any relation between the constituent words in current English and the meaning of the phrase.)