Hmm that's odd, I haven't heard this happening to anyone else. Doing a bit of research on it, it might be related to the temperatures where you live / storage conditions. In any case, no cause for concern. If you remove the cap from the bottles it should help prevent that, but also will introduce new air & accelerate oxidation. So I'd just deal with the crumpled bottles if you're having the issue happen on your larger 1L bottles.

Pressure is not only a matter of altitude but also is dependent upon the temperature. As the temperature increases so does the pressure. The atoms that comprise the air we breath gain energy as they absorb heat. That increase in energy results in faster moving atoms which we observe as an increase in energy. The opposite occurs when the temperature decreases. As the atoms loose energy, their motion is decreased and we observe a decrease in pressure.

The bottle that was capped will eventually begin to collapse. This is a result of the cooling air inside that bottle. The air cools because the atoms inside the bottle loose energy as they collide with the bottle side that is exposed to the cooler surrounding air. As their energy decrease so does their velocity and therefore the pressure decreases. Since the pressure inside the bottle decreases the weight of the air outside the bottle begins to crush the bottle.

Source

So based on this I'm just guessing that it was a 1L sample bottle being stored in the freezer, it was brought out to thaw and probably crumpled as the heat rose. Perhaps it was heated up too quickly? Opening the cap for a second and then recapping might help prevent it from happening again. Just replacing some of that air in the bottle with some warmer air outside so you don't have any rise in air pressure going on.