Chromatography equipment includes hold-up volumes that are external to the packed bed and usually not considered in the development of chromatography models. These volumes can substantially contribute to band-broadening in the system and deteriorate the predicted performance. We selected a bubble trap of a pilot scale chromatography system as an example for a hold-up volume with a non-standard mixing behavior. In a worst-case scenario, the bubble trap is not properly flushed before elution, thus causing the significant band-broadening of the elution peak. We showed that the mixing of buffers with different densities in the bubble trap device can be accurately modeled using a simple compartment model. The model was calibrated at a wide range of flow rates and salt concentrations. The simulations were performed using the open-source software CADET, and all scripts and data are published with this manuscript. The results illustrate the importance of including external holdup volumes in chromatography modeling. The band-broadening effect of tubing, pumps, valves, detectors, frits, or any other zones with non-standard mixing behavior can be considered in very similar ways.