A two-dimensional numerical analysis of a laminar natural convection flow within an air-filled enclosure is proposed in this paper from an unstable configuration previously studied experimentally. The flow is driven by a heated square-section cylinder located at the center of a square-section enclosure. Instabilities are observed for an aspect ratio (height of the cylinder over the height of the cavity) of 0.4 and cause the flow to turn into a three-dimensional and unsteady regime characterized by a symmetry breaking and large scale high amplitude flappings around the cylinder. The multi-physic computational software CEDRE, developed at the ONERA, is used to study this unstable behavior and a time-dependent compressible flow solver is used to perform the two-dimensional simulations under the low Mach number approximation, corresponding to the mid-depth cross-section of the enclosure from the experimental configuration. The first results on the investigation of the first unstable modes confirm the onset of the instabilities at the Rayleigh number of the experiment with asymmetrical motions of the fluid around the cylinder. Further analyses highlight the critical Rayleigh number that defines the instability threshold of the first bifurcation which origin and nature could have been identified. Finally, joint fluid-solid simulations are performed to determine more precisely the role of boundary conditions in the onset of instabilities.