Not really, but it happens all the time. Ultimately, the university just provides you with a piece of paper, of more or less reputational value. Learning is all in your own hands; you've got to own that, and seek out the things you need to know, and learn them. Even at the best universities, and perhaps especially at them, what your professors have experience with will be a decade or more out of date. And this is what your entire career will be about; like Sisyphus, you must continually struggle to push the stone up the hill, and keep abreast of the current technologies and practices. There is no resting on laurels, no complacency.
What if you graduated knowing how to use an IDE, even if you didn't know source control? Or your OS's command line shell? Or a CI tool? Make? Would any one of those things make up for not knowing source control, or would it be unacceptable not knowing all of them?