We derive and validate a set of coupled Bloch wave equations for analyzing the reflection and transmission properties of active semiconductor photonic crystal waveguides. In such devices, slow-light propagation can be used to enhance the material gain per unit length, enabling, for example, the realization of short optical amplifiers compatible with photonic integration. The coupled wave analysis is compared to numerical approaches based on the Fourier modal method and a frequency domain finite element technique. The presence of material gain leads to the build-up of a backscattered field, which is interpreted as distributed feedback effects or reflection at passive-active interfaces, depending on the approach taken. For very large material gain values, the band structure of the waveguide is perturbed, and deviations from the simple coupled Bloch wave model are found.