In this study the origins of premature transition due to oversuction in boundary layers are studied. An infinite row of circular suction pipes that are mounted at right angles to a flat plate subject to a Blasius boundary layer is considered. The interaction between the flow originating from neighbouring holes is weak and for the parameters investigated, the pipe is always found to be unsteady regardless of the state of the flow in the boundary layer. A stability analysis reveals that the appearance of boundary layer transition can be associated with a linear instability in the form of two unstable eigenmodes inside the pipe that have weak tails, which extend into the boundary layer. Through an energy budget and a structural sensitivity analysis, the origin of this flow instability is traced to the structures developing inside the pipe near the pipe junction. Although the amplitudes of the modes in the boundary layer are orders of magnitude smaller than the corresponding amplitudes inside the pipe, a Koopman analysis of the data gathered from a nonlinear direct numerical simulation confirms that it is precisely these disturbances that are responsible for transition to turbulence in the boundary layer due to oversuction.