What I want to know is, on the sample image of molybdenum disulfide (b), there is one atom on the right near the vertical center, that is noticeably dimmer than the rest. What could account for that?
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).
Maybe that one was less reflective than the others?
Pro tip: always polish the atoms when you make record breaking pictures of them.