A two-dimensional (2D) material placed on an atomically flat substrate can lead to the formation of surface nanobubbles trapping different types of substances. In this paper graphene nanobubbles of the radius of 7-34 nm with argon atoms inside are studied using molecular dynamics (MD). All modeled graphene nanobubbles except for the smallest ones exhibit an universal shape, i.e., a constant ratio of a bubble height to its footprint radius, which is in an agreement with experimental studies and their interpretation using the elastic theory of membranes. MD simulations reveal that argon does exist in a solid close-packed phase, although the internal pressure in the nanobubble is not sufficiently high for the ordinary crystallization that would occur in a bulk system. The smallest graphene bubbles with a radius of 7 nm exhibit an unusual "pancake" shape. Previously, nanobubbles with a similar pancake shape were experimentally observed in completely different systems at the interface between water and a hydrophobic surface.