This study investigates the effects of two-dimensional gap induced flow structures on boundary layer transition. Through direct numerical simulations (DNS) and spectral proper orthogonal decomposition (SPOD), we analyze the impact of Rossiter and centrifugal modes on boundary layer transition. The research explores the interactions between these modes and how they contribute to transition mechanisms. Results reveal that while two-dimensional Rossiter modes create memory effects within turbulent flow regions, three-dimensional centrifugal modes add complexity by three-dimensionalizing the flow within the gap. Comparisons with linear stability theory (LST) confirm the presence of these modes, and their interaction hints at scenarios where combined instabilities might drive boundary layer transition. This work enhances the understanding of bypass transition processes caused by surface imperfections, contributing to flow control strategies in aerodynamics.