A bottle of water was emptied, sealed and stored in a cool and dry place by a mountain hiker.?

Increase of air pressure outside the bottle compared to inside. Could be caused by changing atmospheric pressure systems or changes in temperature (air outside may be cooler than air inside the bottle).

not clear if you mean the bottle was left somewhere or carried with the hiker.

For me, the obvious explanation is contraction of the air on temperature decrease. I have seen this sort of thing happen more times than I can count. My son leaves half empty water bottles in the car, and I live in a place that gets pretty cold. The bottles contract over night in the cold, then re-expand on my way to work as the car heats up. I can hear and see it happening.

If she took the bottle with her, it would mean that she hiked up the mountain and air pressure was greater outside the bottle than inside. HOWEVER, it she left it behind in that cool dry place, then she'd sealed it under warmer conditions and upon cooling the air pressure inside became lesser than the air around it.