Microfluidic devices can be used to produce highly controlled and monodisperse double or multiple emulsions. The presence of inner drops inside a jet of the middle phase introduces deformations in the jet, which leads to breakup into monodisperse double emulsions. However, the ability to generate double emulsions can be compromised when the interfacial tension between the middle and outer phases is low, leading to flow with high capillary and Weber numbers. In this case, the interface between the fluids is initially deformed by the inner drops but the jet does not break into drops. Instead, the jet becomes highly corrugated, which prevents formation of controlled double emulsions. We show using numerical calculations that the corrugations are caused by the inner drops perturbing the interface and the perturbations are then advected by the flow into complex shapes.