Geometry calibration is important in securing high spatial resolution in cone-beam CT. They include the distance from the source to the detector (SDD), the distance from the source to the object (SOD), vertical and horizontal shifts in the detector, the detector tilt and rotational angles, and the source scan angle. These geometric parameters should be accurately estimated for high quality image reconstruction. Ball array phantom is widely utilized for such a calibration, and the algorithmic extraction of geometry parameters from the projection of such phantom is well established. However, in practical applications, such methods may encounter challenging problems that may lead to suboptimal calibration. In this paper, we explain three main causes of errors that often occur in a geometry calibration of an offset cone-beam CT system, and provide a remedy that can reduce such errors. The validation of the proposed method was also conducted using a real offset dental cone-beam CT system.