These are probably the two most significant program-impact rumors I heard in the past few years that didn't leak at the time. I can't speak first hand to their veracity, but they're "allegedly" what happened:
The first is what went down with Harry Hiestand. He was a coach who worked guys HARD and two of them (Hoge, Boudreaux) did not like it. Hoge allegedly started keeping a journal documenting "abuse" and when he went to transfer they went to ND and said "sign the waiver or we go public." It worked out for Hiestand getting an NFL gig, but I was told he was likely not to have the option to return to ND because of the complaints about his conduct. Ironically, a lot of the guys credit Hiestand with their development and becoming stars... different strokes for different folks? There was some shit though like spitting on people or whatever that obviously crosses a line if true.
Second, and a lot of this has leaked since, but honestly the Chip Long stuff was crazy. I was surprised that they were able to keep as tight of a lid on that as they did. There was a full on mutiny brewing. Most of our offensive starters on last year's team were allegedly either going to declare for the NFL or transfer if he was retained. Reportedly just a total asshole to everyone who created a super toxic environment. Constantly yelling, constantly belittling people. Per one starter, paraphrasing, "the only motivation to play well was so that you wouldn't get yelled at." He was a BVG level hire on offense, people just didn't realize it at the time because the talent of the players + Kelly + the elite Clark Lea defense had the team winning so much.
Again, everything above is "allegedly" because it's all second hand.