Associated particle imaging (API) utilizes the inelastic scattering of neutrons produced in deuterium-tritium (DT) fusion reactions to obtain 3-D isotopic distributions within an object. The locations of the inelastic scattering centers are calculated by measuring the arrival time and position of the associated alpha particle produced in the fusion reactions, and the arrival time of the prompt gamma created in the neutron scattering event. While the neutron and its associated particle move in opposite directions in the center-of-mass (COM) system, in the laboratory system the angle is slightly less than 180°, and the COM movement must be taken into account in the reconstruction of the scattering location. Furthermore, the fusion reactions are produced by ions of different momenta, and thus the COM velocity varies, resulting in an uncertainty in the reconstructed positions. In this article, we analyze the COM corrections to this reconstruction by simulating the energy loss of beam ions in the target material and identifying sources of uncertainty in these corrections. We show that an average COM velocity calculated using the ion beam direction and energy can be used in the reconstruction and discuss errors as a function of ion beam energy, composition, and alpha detection location. When accounting for the COM effect, the mean of the reconstructed locations can be considered a correctable systematic error leading to a shift/tilt in the reconstruction. However, the distribution of reconstructed locations also have a spread that will introduce an error in the reconstruction that cannot be corrected. In this article, we will use the known stopping powers of ions in materials and reaction cross sections to examine the reconstruction uncertainties. We also discuss the impact of this effect on our API system.