They are still occupied and under Israeli military rule.
They shouldn't be counted separately until they have rule of their own country, not just a rule of the prison grounds.
Gaza is not occupied. Hamas is allegedly in full control there. Israel and Egypt control their borders but Hamas runs Gaza. Hamas completely to blame for the lack of freedoms there.
Palestinians in the West Bank are ruled by the PA except where military matters are involved. The PA is completely responsible for the well documented repression there.
Israel is responsible for checkpoints and whether or not Palestinians can work across the Green Line. The PA are the ones arresting people for facebook posts (just like Turkey has been doing).