Unsupervised source separation involves unraveling an unknown set of source signals recorded through a mixing operator, with limited prior knowledge about the sources, and only access to a dataset of signal mixtures. This problem is inherently ill-posed and is further challenged by the variety of time-scales exhibited by sources in time series data. Existing methods typically rely on a preselected window size that limits their capacity to handle multi-scale sources. To address this issue, instead of operating in the time domain, we propose an unsupervised multi-scale clustering and source separation framework by leveraging wavelet scattering covariances that provide a low-dimensional representation of stochastic processes, capable of distinguishing between different non-Gaussian stochastic processes. Nested within this representation space, we develop a factorial Gaussian-mixture variational autoencoder that is trained to (1) probabilistically cluster sources at different time-scales and (2) independently sample scattering covariance representations associated with each cluster. Using samples from each cluster as prior information, we formulate source separation as an optimization problem in the wavelet scattering covariance representation space, resulting in separated sources in the time domain. When applied to seismic data recorded during the NASA InSight mission on Mars, our multi-scale nested approach proves to be a powerful tool for discriminating between sources varying greatly in time-scale, e.g., minute-long transient one-sided pulses (known as ``glitches’) and structured ambient noises resulting from atmospheric activities that typically last for tens of minutes. These results provide an opportunity to conduct further investigations into the isolated sources related to atmospheric-surface interactions, thermal relaxations, and other complex phenomena.