Ince was charged with three breaches of FA Rule E3, which are alleged to have occurred in or around the tunnel following his side's game at the Goldsands Stadium on Saturday.
The Seasiders won 2-1 but Ince had been sent to the stands in the closing stages after he launched a water bottle in anger when Nathan Delfouneso missed a clear chance to add a third goal.
The charges are that Ince; used abusive and/or insulting words towards a match official; his behaviour towards a match official constituted violent conduct; and that he used threatening words and/or behaviour towards a match official.
Blackpool's assistant manager Rae has also been charged in relation to the same game for an alleged use of threatening behaviour towards a match official in or around the tunnel at the end of the match.
Both Ince and Rae have until 6pm on Thursday to respond to the charges.