Determining the structure of a molecule requires knowing both the amplitude and the phase of the photon wave being diffracted from the crystalline sample. Although a detector can measure the intensity of a wave, which is proportional to its amplitude, there is no way to measure its phase. Thus, when measuring a diffraction pattern it is common to hear that one has "lost the phase." Reconstructing the phase of the diffracted wave is the crux of the phase problem.
See also