We present a detailed atomic-level study of defects in bilayer MoS2 using aberration-corrected transmission electron microscopy at an 80 kV accelerating voltage. Sulfur vacancies are found in both the top and bottom layers in 2H- and 3R-stacked MoS2 bilayers. In 3R-stacked bilayers, sulfur vacancies can migrate between layers but more preferably reside in the (Mo-2S) column rather than the (2S) column, indicating more complex vacancy production and migration in the bilayer system. As the point vacancy number increases, aggregation into larger defect structures occurs, and this impacts the interlayer stacking. Competition between compression in one layer from the loss of S atoms and the van der Waals interlayer force causes much less structural deformations than those in the monolayer system. Sulfur vacancy lines neighboring in top and bottom layers introduce less strain compared to those staggered in the same layer. These results show how defect structures in multilayered two-dimensional materials differ from their monolayer form.