In this work, we highlight the influence of the particle–particle interaction on the retention behavior in asymmetric flow field-flow fractionation (A4F) and the misunderstanding considering the size determination by a light-scattering detector (static and dynamic light scattering) by comparing fullerene nanoparticles to similar sized polystyrene nanoparticle standards. The phenomena described here suggest that there are biases in the hydrodynamic size and diffusion determination induced by particle–particle interactions, as characterized by their virial coefficient. The dual objectives of this paper are to (1) demonstrate the uncertainties resulting from the current practice of size determination by detectors coupled to an A4F system and (2) initiate a discussion of the effects of particle–particle interactions using fullerene nanoparticles on their characterization as well as their origins. The results presented here clearly illustrate that the simple diffusion coefficient equation that is generally used to calculate the hydrodynamic size of nanoparticles (NPs) cannot be considered for whole fractograms according to their size distribution. We tried to identify particle interactions that appear during fractionation and demonstrated using the fully developed diffusion coefficient equation. We postulate that the observed interaction-dependent retention behavior may be attributed to differences in the virial coefficient between NPs and between NPs and the accumulation wall (membrane surface) without quantifying it. We hope that our results will stimulate discussion and a reassessment of the size determination procedure by A4F-LS to more fully account for all the influential material parameters that are relevant to the fractionation of nanoscale particles by A4F.