Comment by albutr

It's a chalcogen vacancy, a very common type of defect in these materials. These materials are called transition metal dichacogenides, so they have the form MX2, where M is a metal (most commonly Mo or W) and X is a chalcogen (typically S or Se). In this case, there is an S missing, but you still see a spot because there is another S below it (if you look at the crystal structure, it resembles graphene but has more complex structure in the third dimension, its 3 atoms thick rather than being flat, with the two chalcogens in the unit cell right on top of each other).