There are several possible sources of error in your setup, including the fact that the Steinhart-Hart equation is just an approximation for the thermistor behavior.
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Have you calibrated your resistor/thermistor combination against known temperatures?
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Are you using the best possible coefficients for the Steinhart-Hart approximation, for that particular thermistor/resistor combination?
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Are you exceeding the temperature range over which the S-H coefficients are accurate?