We derive a coupled mode theory for the interaction of an optical cavity with a waveguide that includes waveguide dispersion. The theory can be applied to photonic crystal cavity waveguide structures. We derive an analytical solution to the add and drop spectra arising from such interactions in the limit of linear dispersion. In this limit, the spectra can accurately predict the cold cavity quality factor (Q) when the interaction is weak. We numerically solve the coupled mode equations for the case of a cavity interacting with the band edge of a periodic waveguide, where linear dispersion is no longer a good approximation. In this regime, the density of states can distort the add and drop spectra. This distortion can lead to more than an order of magnitude overestimation of the cavity Q.