Surface irregularities such as steps, roughness and waviness can have a significant impact on the laminar-to-turbulent transition process over wings and tails of commercial aircraft. In this work, the effect of forward-facing steps (FFS) on subsonic crossflow-vortex-dominated boundary layers is investigated. The geometry under study is a swept-wing, which reproduces the experimental setup of Rius-Vidales in the Low Turbulence Tunnel (LTT) at the Delft University of Technology. The setup is characterized by the presence of a forward-facing step with different heights. Results from direct numerical simulations (DNS), conducted in previous work on this geometry, are here employed as the base flow for the instability analysis. In particular, two-dimensional linear stability theory (LST-2D) and three-dimensional parabolized stability equations (PSE-3D) are employed to study the influence of two step heights on the secondary instabilities of crossflow vortices and identify how those perturbations change compared to the case without step. Furthermore, the analysis aims to assess the instability characteristics of the flow in the region downstream of the step and to identify the unstable disturbances that are developing. In order to cope with a base flow that is periodic in the direction parallel to the leading edge and features a slow variation along the crossflow- vortex axis, the stability problem is formulated in a non-orthogonal coordinate system.