In this paper, the techniques of Data Reconciliation and Gross Error Detection have been applied to a MGT/HTFC (Micro Gas Turbine / High Temperature Fuel Cell) hybrid system emulator test rig installed and operated by N.E.T.L. (National Energy Technology Laboratory), West Virginia (USA). The plant includes two counter-flow heat exchangers working in parallel: theoretically, they should work in the same way, that is same mass flow rates and same temperature differences between hot and cold side; from various tests carried out on the plant, non-symmetrical operation has been often highlighted by measurements. The hardware redundancy of measurements and equations allowed the data reconciliation and gross error detection techniques to be employed. Gross Error Detection has been applied to identify the presence of some possible systematic gross errors in the data: no gross error has been found. Data Reconciliation allowed to significantly improve the accuracy of the estimation of the recuperator unbalance, mainly in terms of mass flow rate. The mass flow unbalance has been detected with sufficient level of confidence, and can now be used to better investigate such a phenomenon.