There could be a consistent bias due to the placement of the thermometer. You can't expect the LLM to assume that the temperature of the water means the temperature in a bottom corner of the cup which I guess is where the thermometer's sensor was. If he had told it how he would place the thermometer, then it could have known that, otherwise, what if it's being clever and finding an average temperature or one that would be measured at some other location? This seems qualitatively consistent with the fact that most models predicted higher temperature than what he measured because of hot water rising and cooling being greatest near the walls of the cup.

This isn't really uncertainty so much as not defining the meaning of "temperature of the water".