The effects of a background state, or states, on stimulated Raman adiabatic passage (STIRAP) processes are investigated. The study is based on a realistic model of the laser-assisted $\mathrm{HCN}\to \mathrm{HNC}$ isomerization process. While the high density of states in the energy regime above the isomerization barrier plays an important role, the strong variation of the transition dipole moments connecting these states with the localized HCN and HNC states is shown to be more significant in determining the success or failure of the STIRAP process. Therefore, care must be taken when proposing the use of STIRAP-based schemes to control molecular excitation especially when control is justified via few-level models.