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An efficient control system is paramount for the operability of Fuel Cell systems since, in ideal cases, it allows the regulation of power output, temperatures and economic performance under a dynamic working environment where they need to operate. Although several control strategies, scenarios and methodologies have been broadly investigated, it is usually taken for granted that the measurements from the system, necessary for the control feedback, are correct. Nonetheless, when simple thermocouples are used to measure gas temperatures there is a significant danger of systematic errors due to radiation effects between the surroundings and the thermocouple. The discrepancy between a real gas temperature and the one measured depends mainly on the temperature difference between the gas and the solids around as well as the gas velocity, radiation factors etc. The phenomenon has been described in our past publications. In this work we simulate an SOFC system and apply control scenarios in order to investigate potential problems arising from such systematic errors. The results show that important dysfunctions may occur and caution should be applied in design of both control and of the systems themselves.