Quantum corrections to electrical resistance can serve as sensitive probes of the magnetic landscape of a material. For example, interference between time-reversed electron paths gives rise to weak localization effects, which can provide information about the coupling between spins and orbital motion, while the Kondo effect is sensitive to the presence of spin impurities. Here we use low-temperature magnetotransport measurements to reveal a transition from weak antilocalization (WAL) to Kondo scattering in the quasi-two-dimensional electron gas formed at the interface between SrTiO$_3$ and the Mott insulator NdTiO$_3$. This transition occurs as the thickness of the NdTiO$_3$ layer is increased. Analysis of the Kondo scattering and WAL points to the presence of atomic-scale magnetic impurities coexisting with extended magnetic regions that affect transport via a strong magnetic exchange interaction. This leads to distinct magnetoresistance behaviors that can serve as a sensitive probe of magnetic properties in two dimensions.