Raymond Zeitler has an interesting post on an aspect of using Org Mode code blocks that I didn’t know about. Zeitler says that he prefers to write his code in separate code files rather than in Org mode code blocks and provides an example of why that is.
The TL;DR is that in certain edge cases, things like differing syntax tables can make code behave differently in Org mode than it does directly in Emacs. Take a look at his post for the details.
I have to say that I’ve never run into this problem. Perhaps that’s because I usually use Org code blocks only for code that will be executed in the Org environment. The few times that I have run the code outside of Org, I haven’t run into the problems that Zeitler describes.
Your mileage may vary, of course, but it’s good to be aware that there are some edge cases that can reach out and bite you if you’re not careful. Most of you, I’m sure, will have my experience but it pays to be aware of what can go wrong.