What are you feeding her?
Over time the puppy expands what it thinks its territory is. For example, when you first get the pup at 7 wks, it will think its territory is its crate but not outside the crate in the room. Then it may expand on that and decide its territory is the entire room as well as the crate, but not the garden. Some dogs expand further and won't toilet even in their own garden, because that becomes their own 'territory' - they will only go outside. Some don't reach this extreme.
It may be that your dog now considers inside to be her territory. She doesn't want to mess inside because that is fouling her own territory, but she really needs to toilet, so she has to mess inside. This distresses her extremely, so she tries to take the mess away and hide it or bury it somewhere.
At 9 months she should be able to go through the night without needing the toilet, though, and should not need paper put down for her any more!! Does she toilet during the day? When is the last time you feed her at night? Why don't you feed her earlier at night, take her out and give her a good chance to toilet before you go to bed, then shut her in the crate at night. If you want to be extra sure, get up in the middle of the night and take her out, as you would do for a new puppy.