Scattering of ultrashort X-ray pulses (USP) is an important component of the diffraction analysis of matter using modern USP sources. Usually, the specific scattering of such USPs is not taken into account to determine the structure of a substance. Taking into account the specifics of scattering on complex structures will give more accurate results when deciphering complex structures. In this work, it is shown that when X-ray USPs are scattered on diamond with NV centers, it is necessary to take into account the pulse duration. The results obtained can be very different from the widely used theory of diffraction analysis, which confirms the need to take into account the specifics of USP scattering when diagnosing complex structures. It is also shown that scattering spectra are quite sensitive to the concentration of NV centres in the diamond structure and this can be used in diffraction analysis.