It's particularly difficult with most proteins and other biomolecules. [0] But even for small molecular compounds, it isn't always easy. I'm not sure about growing high quality crystals of metal-organic frameworks, but they could easily be limited by defects. Some compounds might be too waxy if there are long aliphatic chains involved.
Even if you do get decent-looking crystals, they might be twinned. If you are working with air or water sensitive compounds, they need to be handled with extreme care and might degrade before the data collection is complete. Some might also have temperature sensitivity, such that they need to be kept at -20 C to prevent melting or another phase transition.
Overall it can be a real make-or-break issue for someone engaged in chemical research.
[0] Check out this PDF of a PowerPoint on the topic: https://hamptonresearch.com/uploads/documents/ramc/RAMC2011_...
Also, it looks like they are changing the topic each year to follow the current fashion, and they are publishing like 200 papers per year, so $50K is like $250 per paper. My (totally unsupported) guess is that they are charging a few hundred bucks per paper, so using a real diffractometer to make a new unique fake image for each paper would duplicate the price of each paper.