The diffraction pattern is due to elastic scattering from the "ion core", which is the stationary net charge of the atomic nucleus and it's bound electrons;  these elastically scattered electrons don't lose any energy. The electrons which interact with the free electrons are inelastically scattered, and contribute a foggy background to the diffraction pattern.

An electron which scatters more than once contributes to the background,  so very thin crystals are used in transmission.  For my research I found 100 nm worked well for gold and platinum, and several hundred nm for graphite.

Because of the energies involved this latter process may eject some of the free electrons, or generate x-rays. For an electron microscope the energies may vary from 20 to 200 keV or more; for low energy electron probes the electrons may have only a few eV.

There are many valuable applications for electron probes, including imaging, diffraction, and analysis. Electrons, x-rays, and neutrons each has it's own unique advantages. Electrons require ultrahigh vacuums, while x-rays can be done in air; electrons have much shorter wavelengths than x-rays of the same energy, and interact more strongly. In addition,  it is easy to focus electrons, which allows you to image the surface.