We consider a deep matrix factorization model of covariance matrices trained with the Bures-Wasserstein distance. While recent works have made advances in the study of the optimization problem for overparametrized low-rank matrix approximation, much emphasis has been placed on discriminative settings and the square loss. In contrast, our model considers another type of loss and connects with the generative setting. We characterize the critical points and minimizers of the Bures-Wasserstein distance over the space of rank-bounded matrices. The Hessian of this loss at low-rank matrices can theoretically blow up, which creates challenges to analyze convergence of gradient optimization methods. We establish convergence results for gradient flow using a smooth perturbative version of the loss as well as convergence results for finite step size gradient descent under certain assumptions on the initial weights.