I encountered two instances over the years where plastic bottles/jugs of milk had a brown sediment settled at the bottom. It turned out to be cocoa particles, presumably from carryover of chocolate milk production at the same facility. Chemical analyses showed the presence of theobromine, Extraneous chemical contaminants were absent. Also, the color (a specific shade of brown) was a dead giveaway. Isolation of the unknown substance was hampered because the material got resuspended during shipment to the lab, and by Microbiology testing prior to Chemistry testing (their protocol requires thoroughly shaking the containers before getting their sub-sample).

Photos of bottom of the milk jug sticking out from a shelf


Small portion in test tube spun down in a centrifuge



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Here are 2 references discussing the physical stability problem of cocoa particles during chocolate milk production

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