Graphene on silicon carbide (SiC) bears great potential for future graphene electronic applications because it is available on the wafer-scale and its properties can be custom-tailored by inserting various atoms into the graphene/SiC interface. It remains unclear, however, how atoms can cross the impermeable graphene layer during this widely used intercalation process. Here we demonstrate that, in contrast to the current consensus, graphene layers on SiC are not homogeneous, but instead composed of domains of different crystallographic stacking. We show that these domains are intrinsically formed during growth and that dislocations between domains dominate the (de)intercalation dynamics. Tailoring these dislocation networks, e.g. through substrate engineering, will increase the control over the intercalation process and could open a playground for topological and correlated electron phenomena in two-dimensional superstructures.