It separated or wheyed off
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Whey on a yogurt is usually normal
A clear or slightly cloudy liquid on the surface of a set yogurt is whey that the protein network has expelled. It is harmless, it can be stirred back in or poured off, and it is more pronounced in products with lower solids. Told about it, buyers accept it; not told, they read it as spoilage.
Unless it is excessive, in which case look at the set
A lot of whey usually means the gel is weak, which takes you back to the set page: incubation temperature, culture activity or milk composition. Disturbing a set yogurt while it is still warm also breaks the network and produces this, which is a handling cause rather than a process one.
Sediment in a plant beverage is the default behavior
The solids are suspended rather than dissolved, and gravity acts on them. Without a stabilizer this happens in a day. It is not a fault and it is a commercial problem, because a buyer pouring cloudy water from the top of the bottle has had a bad experience regardless of the explanation.
Shake before use only goes so far
It works if the sediment is loose. If it has compacted into a layer at the bottom, shaking does not recover it and the last part of the container pours thick. That is the point at which a stabilizer stops being optional for a retail product.
The container shape matters for both
A narrow base concentrates sediment where it is hardest to redisperse, and a wide mouth lets somebody stir a yogurt properly. These are not large effects individually and they decide how the product performs in the hand rather than on the shelf.