Is it considered misconduct to omit a university that you were enrolled in, but didn't attend any classes at, on graduate application? Is it considered an academic misconduct to skip listing a university's name in the graduate application, in which somebody got admission but never attended any class/lab/test/exam whatsoever and as a result his transcript is shown failed in all courses in one semester?
Whether someone has performed "academic misconduct" is something that a specific body of people must decide upon using both general principles of academic ethics and the specific rules of the academic body in question. It depends at least a bit on who is doing the considering.  So it seems better to think in terms of whether certain actions could reasonably or likely be construed as academic misconduct by certain parties.

When it comes to graduate admission, the relevant academic parties are the admissions committee and the authorities (faculty, administration...) of the institution.  It depends a bit on what the application asks for.  If you are asked to supply all college/university level transcripts (a common request) and intentionally omit some, then certainly you are behaving dishonestly in the usual sense.  Whether the dishonesty will be construed as academic misconduct if discovered is up to the relevant academic parties to decide, but: yes, there is a real risk of that happening.

You make it sound like "somebody" got a bit of a raw deal by getting failing grades for classes that were never attended whatsoever.  If somebody never showed up at all, then it seems like there is a good case that the enrollment was some kind of misunderstanding and that grades should not have been given.  Somebody should seek to fix that with the institution that issued the failing transcript.  It will probably be at least a certain amount of fuss -- e.g. contacting every instructor to get them to confirm that the student was a pure no-show.  If somebody's best efforts do not suffice to resolve the question, the ethical thing to do -- and the path which nullifies any claims of academic misconduct -- is to include the transcript together with an explanation of what happened, possibly along with parties to contact for additional corroboration.