The most serious of any NCAA violations that the NCAA will perceive, is when members of the institution - the athletic department, or the coaching staff - do not cooperate fully with NCAA investigators. The NCAA EXPECTS those institutional representatives to not only work with NCAA investigators, but to take the lead in determining what was done in violation, and in taking measures to ensure they don't happen again.
It's why when institutions are determined to go overboard in their cooperation, they generally get favorable findings and penalties from the NCAA. Examples that are related with South Carolina, were the Whitney Hotel scandal, where the NCAA accepted self-imposed penalties from USC and did not add anything more. Also was the FBI investigation into college basketball involving ASM Sports rep Christian Dawkins, where South Carolina was removed early on from the investigation due to our handing over everything and then some in the way of records and texts to the FBI, and the NCAA followed suit.
But when an institution refuses to work with the NCAA, or gives the NCAA the run-around, then the NCAA typically goes all in on that program under investigation, without the use of vaseline. They took away Georgia Tech's ACC FB title because members of its AD obstructed their investigation. They hit former Tennessee MBB head coach Bruce Pearl hard because he lied about a BBQ cookout he had for prospects and their families in violation of NCAA rules.
Expect Harbaugh and Michigan to get the heavy-handed treatment, if they actually lied and refused to cooperate with them with their investigation.....