Register control of roll-to-roll printing system for printed electronics requires accurate measurement of register errors. The register marks used for the recognition of patterns position between layers have inherently defects due to low printability of register marks themselves, which brings out inaccurate register accuracy and consequently low performance of printed electronics devices. In this study, the compensation methods for the unrecognized or missing register data are proposed to improve the recognition and consequently the control performance of register accuracy in roll-to-roll printing equipment. The compensation methods using the prior data and the linear interpolation are proposed and compared with the case without compensation for the simulation as well as experiment. Only the linear interpolation method could successfully compensate the missing data and consequently improve the register control performance. We should apply the compensation process of the register errors to improve the register control accuracy in the roll-to-roll printing equipment.