We present a parametric study of the unsteady phenomena associated with the flow of elongated gas bubbles travelling through liquid-filled square capillaries under highWeber number conditions. These conditions induce the formation of an indentation at the back of the bubble that commonly gives way to a deep re-entrant liquid jet penetrating the bubble. Subsequent steps include pinch-off events in the penetrating liquid to generate one or multiple encapsulated drops which may coalesce, in conjunction with the bursting of the bubble-liquid interface by either the liquid jet or the drops. Some of these interfacial instabilities have previously been reported experimentally [65] and numerically [43] for liquid-liquid flow in microchannels. We carry out three-dimensional direct numerical simulations based on a hybrid interface-tracking/level-set method capable of accounting for the presence and dynamic exchange of surfactants between the liquid bulk phase and the liquid-gas interface. Our results indicate that the delicate interplay amongst inertia, capillarity, viscosity, surfactant adsorption/desorption kinetics, and Marangoni stresses has a dramatic influence over the non-axisymmetric morphological structures of the encapsulated drops-elongated bubble. This strong coupling also influences the pinch-off time, penetration depth of the liquid, and number, size, and velocity of the encapsulated drops across the bubble. The observed phenomena are summarised in three main morphological regimes based on surfactant-related parameters and dimensionless groups. A discussion of the flow regime maps is also provided.