I can't say that this is a sign of what's to come but the bad behavior of an Exec toward his board, e.g. firing them when confronted over hiring his daughter for a fairly good wage although we don't know that she wasn't worth every penny.
It appears from the Boston Globe article that the board and staff went to the Attorney General. Following an investigation, the Attorney General ruled that the "nonprofit's governance structure did not assure an independent board that was free from management’s direction. Therefore, the governance structure did not comply with good governance standards for nonprofit charitable boards."
Without more details it's hard to say how such a case would end up at the AG's level were it not for the reporting of disgruntled board and staff. But with more scrutiny via charity watchdogs and a slightly more attentive IRS with the newly revised 990's, it's possible that boards and execs alike should consider bad behavior more suspect to review and judgement in the coming years.