Marine low‐level clouds continue to be poorly simulated in models despite many studies and field experiments devoted to their improvement. Here we focus on the spatial errors in the cloud decks in the Department of Energy Earth system model (the Energy Exascale Earth System Model [E3SM]) relative to the satellite climatology by calculating centroid distances, area ratios, and overlap ratios. Since model dynamics is better simulated than clouds, these errors are attributed primarily to the model physics. To gain additional insight, we performed a sensitivity run in which model winds were nudged to those of reanalysis. This results in a large change (but not necessarily an improvement) in the simulated cloud decks. These differences between simulations are mainly due to the interactions between model dynamics and physics. These results suggest that both model physics (widely recognized) and its interaction with dynamics (less recognized) are important to model improvement in simulating these low‐level clouds.