The best explanation for the observed phenomenon is:
The cocoa was mixed with hot water, but some cocoa settled as it cooled because the solubility went down.
When the hot cocoa was initially made, cocoa powder dissolved well in the hot water due to higher solubility at elevated temperatures. However, as the cocoa cooled down, the solubility of the cocoa powder decreased, causing some of it to precipitate out and settle to the bottom of the mug.