When an in-plane field is applied to a clean interface superconductor, a Fulde-Ferrell-Larkin-Ovchinnikov (FFLO)-like phase is stabilized. This phase has a U(1)×U(1) symmetry and, in principle, this symmetry allows for flux carrying topological excitations different from Abrikosov vortices (which are the simplest defects associated with S1 → S1 maps). However, in practice, largely due to electromagnetic and other intercomponent interactions, such topological excitations are very rare in superconducting systems. Here, we demonstrate that a realistic microscopic theory for interface superconductors, such as SrTiO3/LaAlO3, predicts an unconventional magnetic response where the flux-carrying objects are skyrmions, characterized by homotopy invariants of S2 → S2 maps. Additionally, we show that this microscopic theory predicts that stable fractional vortices form near the boundary of these superconductors. It also predicts the appearance of type-1.5 superconductivity for some range of parameters. Central to these results is the assumption that the Rashba spin-orbit coupling is much larger than the superconducting gap.