The impact of trench defects in blue InGaN/GaN light emitting diodes (LEDs) has been investigated. Two mechanisms responsible for the structural degradation of the multiple quantum well (MQW) active region were identified. It was found that during the growth of the p-type GaN capping layer, loss of part of the active region enclosed within a trench defect occurred, affecting the top-most QWs in the MQW stack. Indium platelets and voids were also found to form preferentially at the bottom of the MQW stack. The presence of high densities of trench defects in the LEDs was found to relate to a significant reduction in photoluminescence and electroluminescence emission efficiency, for a range of excitation power densities and drive currents. This reduction in emission efficiency was attributed to an increase in the density of non-radiative recombination centres within the MQW stack, believed to be associated with the stacking mismatch boundaries which form part of the sub-surface structure of the trench defects. Investigation of the surface of green-emitting QW structures found a two decade increase in the density of trench defects, compared to its blue-emitting counterpart, suggesting that the efficiency of green-emitting LEDs may be strongly affected by the presence of these defects. Our results are therefore consistent with a model that the "green gap" problem might relate to localized strain relaxation occurring through defects.