Why do water bottles shrink when they freeze?
When I left a half-full water bottle in the car overnight during winter here in Virginia and it froze, the bottle contracted around the ice that formed and got misshapen and sucked in on one side. So instead of looking like a circle from the top, it had an oval shape. My husband and I thought that water expands when it freezes, so why should the bottle crumple around the ice rather than keeping an uniform circle shape that would be suggested by expansion?
I would say that it's the air inside the bottle also contracting.
Air gets bigger as it gets warmer and smaller as it gets colder.
So, although you're right that water expands when it freezes, the air will also shrink down. And if you have a good seal on your bottle so that no more air can creep in, I think that it might crumple when it got colder.
The material of the bottle itself might even contract when it gets cold, which would crumple the bottle into a distorted shape.