I keep all my water and juice drinks under the counter, lots of them, because they keep.
I had a plastic gallon of water underneath the counter that got left behind a little and ignored. I took it out of the back today, and it is shriveled and vacuumed down to 1/3 size, with water in it.
The water didn’t leak out in a normal way. It is held fairly well by the seal. It smells musty and the area smells that way but it’s not saturated or soaked.
How does this happen?
Sounds like a slow leak, though I’m not sure of the physics behind plastic container shriveling/shrinkage in such circumstances.
I’ve had at least one plastic one gallon water jug spring a slow leak in storage and eventually empty. They’re just not very sturdy over the long term.
Fill the bottle back up with air, cap it, and squeeze it. You’ll likely find a tiny pinhole on it somewhere. (I reuse gallon and half-gallon jugs for water storage, and this happens sometimes for no apparent reason.)
I take it that the last time the container was filled it wasn’t with hot water? That would be one easy way the container could shrivel, as the interior cooled.
This has to do with the bottle cap. For cheap beverages (and beverages that are not known to spoil), the bottle cap is a simple one way valve. Take off the bottle cap and you will see a soft lining material. The soft lining lets the gases out of the bottle when there is over-pressure (like a warm bottle) but it does not let gases back in when there is underpressure. So if your house temperature goes warm (evenings and weekend when at home) and cold (other times when you are not at home) the bottle will keep losing gases and shrivel up. They call this paneling.
More here http://www.pearceplastics.com/venttech.html. Google paneling of plastic bottles for better explanations / theories 
Aha!! So that’s the dealio! I had this happen to a 2 1/2 gallon Iced Mountain bottle of water I kept forgetting in my truck over a considerable period of time. It was collapsed and virtually empty, but the seal over the spout wasn’t broken. I braced myself for a soaked trunk, but it wasn’t wet at all. Bizarre!
The counter is next to the stove. Anomaly explained.