First his team gave up 38 unanswered points in a loss to UCLA on Saturday, after being up 21-3 late in the second quarter.
Then it was a feud with former Husker great Tommie Frazier - who won two national championships with the Huskers.
But things might have even got worse for Pelini on Monday afternoon.
Deadspin.com posted audio of the sixth-year head coach being very critical of Nebraska fans and the Omaha World Herald after a come from behind victory over Ohio State in 2011.
Disclaimer: The audio contains strong language.
Courtesy: Omaha World Herald
On Monday evening, Pelini released a statement apologizing for his comment.
"I want to sincerely apologize for my comments from two years ago which became public today," Pelini said in the statement. "I take full responsibility for these comments. They were spoken in a private room following the Ohio State game. I was venting following a series of emotional events which led to this moment. That being said, these comments are in no way indicative of my true feelings. I love it here in Nebraska and feel fortunate to be associated with such a great University and fan base. I again apologize to anyone whom I have offended."
Nebraska athletic director Shawn Eichorst also released a statement on Monday in response to the posted audio.
"I am disheartened and disappointed by the 2011 comments published today attributed to Coach Pelini about our dedicated and passionate fans and supporters," said Eichorst in the statement. "I have spoken with Chancellor [Harvey] Perlman and I have addressed the situation with Bo and expressed our deep concern."
In the same university email, Perlman said he is in discussions with Eichorst on how Nebraska will be "addressing the issue."
This is a developing story. Stay close to Big Red Report for all the latest.