I have heard from my peers on more than one occasion that it is "advised" not to do version controlling of your code from within the IDE where you write it. I have seen them developing on Eclipse, IntelliJ IDEA, etc. but doing version control (in my current scenario - Git) from command-line or standalone clients as opposed to using the corresponding plugins readily available for the IDE.
Though I have used version control plugins in Eclipse and never found any issues, I would like to know what is the general norm and why?