Coordinate measurement gages dominate in the area of dimensional control and variation reduction of automotive body assembly processes. However, coordinate measurement gages do not have the capability to track certain measured features. This incapability introduces inherent measurement error created by part (feature) mislocation in constrained non-measured directions. This inherent measurement error weakens the methods used for process control and variation reduction. In this paper, a principle of measurement uncertainty is developed in order to estimate the measurement error caused by this deficiency. The developed principle describes measurement error, which is independent of any other error related to the mechanical or optical coordinate measurement machines (CMMs, OCMMs). Additionally, an error map determined by the measurement uncertainty principle is created for error compensation. Simulations and two case studies in the area of automotive body assembly process control and variation reduction illustrate the proposed method.