When water becomes ice, it forms crystals. These ice crystals are like any other crystal and can’t just grow anywhere, but instead require a so called “nucleation” point. This can be a tiny little particle or some other activity within the water (in this case). Ice will then form from said nucleation point.
With your bottle, it was below freezing point, but had no nucleation point and thus no ice. This is called super freezing. The way you removed it from the freezer caused a disturbance which resulted in the nucleation point being at the top of the bottle. From there on our all the water formed crystals towards the bottom.
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