We study the fully nonlinear, nonlocal dynamics of two-dimensional vesicles in a time-dependent, incompressible viscous flow at finite temperature. We focus on a transient instability that can be observed when the direction of applied flow is suddenly reversed, which induces compressive forces on the vesicle interface, and small-scale interface perturbations known as wrinkles develop. These wrinkles are driven by regions of negative elastic tension on the membrane. Using a stochastic immersed boundary method with a biophysically motivated choice of thermal fluctuations, we investigate the wrinkling dynamics numerically. Different from deterministic wrinkling dynamics, thermal fluctuations lead to symmetry-breaking wrinkling patterns by exciting higher order modes. This leads to more rapid and more realistic wrinkling dynamics. Our results are in excellent agreement with the experimental data by Kantsler et al. [Kantsler et al., Phys. Rev. Lett., 2007, 99, 17802]. We compare the nonlinear simulation results with perturbation theory, modified to account for thermal fluctuations. The strength of the applied flow strongly influences the most unstable wavelength characterizing the wrinkles, and there are significant differences between the results from perturbation theory and the fully nonlinear simulations, which suggests that the perturbation theory misses important nonlinear interactions. Strikingly, we find that thermal fluctuations actually have the ability to attenuate variability of the characteristic wavelength of wrinkling by exciting a wider range of modes than the deterministic case, which makes the evolution less constrained and enables the most unstable wavelength to emerge more readily. We further find that thermal noise helps prevent the vesicle from rotating if it is misaligned with the direction of the applied extensional flow.