A method operates a three-dimensional (3D) metal object manufacturing system to compensate for errors that occur during object formation. In the method, thermal image data and dimensional image data of a metal object being formed by the 3D metal object manufacturing system is generated prior to completion of the metal object. Thermal conditions are identified from these data and compared to predetermined ranges corresponding to the identified thermal conditions to identify one or more errors. For identified errors outside a corresponding predetermined difference range, the method performs an error compensation technique. The error compensation includes modification of a surface data model, modification of machine-ready instructions, or operation of a subtractive device.