We investigate experimentally the causes of jet plume instability and enhanced mixing observed in the exhaust of shock-containing convergent-divergent nozzles. Key features of the internal flow are the separation shock, separation shear layers, and pattern of alternating expansion and compression waves downstream of the shock. We focus on two possible reasons for this instability-the motion of the separation shock and the wave pattern downstream of the shock. The nozzle flow was generated in a planar facility with variable area ratio and pressure ratio, and the motion of the shock was tracked using time-resolved wall pressure measurements. The isolated effect of the wave pattern was investigated in a separate facility wherein a sonic shear layer, simulating the nozzle separation shear layer, was disturbed with compression and expansion waves emanating from a wavy wall. In both instances, the instability of the shear layer was characterized by time-resolved measurements of the total pressure. In the nozzle flow, the amplitude of shock motion increases with shock strength. Correlation of shock motion with shear layer total pressure is virtually absent for weak shocks but becomes significant for strong shocks. However, impingement of stationary waves on the shear layer had no impact on its growth rate. We conclude that the enhanced shear layer instability is strongly coupled to shock motion, and that the wave pattern by itself is not a cause of enhanced mixing. The occurrence of asymmetric separation at large shock strengths is a further contributor to the enhancement of instability.