This study focuses on direct numerical simulation of imbibition, displacement of the non-wetting phase by the wetting phase, through water-wet carbonate rocks. We simulate multiphase flow in a limestone and compare our results with high-resolution synchrotron X-ray images of displacement previously published in the literature by Singh et al. (Sci Rep 7:5192, 2017). We use the results to interpret the observed displacement events that cannot be described using conventional metrics such as pore-to-throat aspect ratio. We show that the complex geometry of porous media can dictate a curvature balance that prevents snap-off from happening in spite of favourable large aspect ratios. We also show that pinned fluid-fluid-solid contact lines can lead to snap-off of small ganglia on pore walls; we propose that this pinning is caused by sub-resolution roughness on scales of less than a micron. Our numerical results show that even in water-wet porous media, we need to allow pinned contacts in place to reproduce experimental results.