The row erupted after O’Donoghue, who was riding the pacemaker Red Rock Canyon in the Group 1 event, was seen to move off the rail which enabled Johnny Murtagh and stablemate Duke Of Marmalade to go through take the gap and eventually win the race.
O'Donoghue could be found guilty of making a manoeuvre in the interests of a horse from the same stable.
And Ballydoyle mestro O’Brien will need to satisfy the stewards he instructed his rider to treat every other horse in the race without favour.
Murtagh could also be in trouble if the disciplinary panel consider he instructed, directed or encouraged O’Donoghue to ride in the way he did.