There are a number of possible reasons for the difference, in addition to possible calibration errors. Firstly, the thermocouple might not be in good thermal contact with the surface of the sample, or there might be temperature gradients within the sample. If this is the case then the thermocouple and radiation thermometer will not be measuring the same temperature. Alternatively, if the emissivity of the sample is low, or not precisely known, the temperature measured by the radiation thermometer will not represent the true temperature of the sample, again leading to differences. Also, if the sample is small, it might not be fully filling the field-of-view of the radiation thermometer, and the radiation thermometer temperature will therefore be low compared to that of the thermocouple