Because of the loss of IR radiation, nearly all thermopile instruments typically have a negative offset. This offset is most easily visible at night-time, when a small negative value is read instead of zero. This same offset is present during the daytime, but it is not as visible because of the large solar signal.
Another common issue involves leveling an instrument. Leveling a thermopile instrument can cause errors in the direct beam component because the cosine response is not correct. These errors are more notable when the sun is close to the horizon because the angle is so shallow.