Crystal Lattice Defects
First of all, there are no such thing as a "perfect" crystal. 

Defects occur from both human error and the experimental setup.

Defects from human error are primarily due to handling issues, which can never be perfected, especially not if the crystals are solvated.  

Experimental defects can occur from either the diffraction experiment or the crystal growth experiment. Impurities can affect crystal growth by displacing the molecule of interest in the lattice and unless you are attempting neutron diffraction, the crystal will be significantly damaged during the data collection. 

In my field of protein x-ray crystallography, the typical crystals can have diffraction ranging from nothing at all to ~0.8 Angstrom range (best cases) and as such you can have beautiful crystals that have no diffraction and ugly crystals that diffract very well.

Crystal defects can be perfectly acceptable and are a so common that we usually don't think about them too much.