We study the dynamics of a single vortex and a pair of vortices in quasi two-dimensional Bose-Einstein condensates at finite temperatures. To this end, we use the stochastic Gross-Pitaevskii equation, which is the Langevin equation for the Bose-Einstein condensate. For a pair of vortices, we study the dynamics of both the vortex-vortex and vortex-antivortex pairs, which are generated by rotating the trap and moving the Gaussian obstacle potential, respectively. Due to thermal fluctuations, the constituent vortices are not symmetrically generated with respect to each other at finite temperatures. This initial asymmetry coupled with the presence of random thermal fluctuations in the system can lead to different decay rates for the component vortices of the pair, especially in the case of two corotating vortices.