Magnetic dynamics at the nanoscale provide crucial insight into the behavior of superconductors. Using single-spin scanning quantum microscopy, we probe vortex dynamics in the two-dimensional superconductor NbSe2. Our measurements reveal a disordered vortex glass phase that melts near the critical temperature and displays cooling-rate-dependent configurations. Surprisingly, magnetic noise persists well below 𝑇𝑐, with a strength that increases at lower temperatures—contrary to expectations. This behavior, detected via spin decoherence, points to an intrinsic origin driven by competition between supercurrent density and thermal fluctuations. Our results establish single-spin microscopy as a powerful platform for investigating fluctuations in 2D superconductors.