The former England international's Tangerines crashed out of the cup after Tom Clarke scored the hosts' winner three minutes from time at Deepdale, where the final whistle was met with a pitch invasion that saw a steward trampled on by a police horse.
An FA Statement said: "It is alleged that Ince's comments were in breach of FA Rule E3 in that they called into question the integrity of the match referee and/or implied that the match referee was motivated by bias; and/or brought the game into disrepute."
Ince has until Tuesday at 6pm to respond to the charge.
The development comes just a day on from Ince's son, Thomas, being handed a two-match ban by the FA after the England Under-21 forward accepted a charge for using an offensive and/or insulting and/or abusive gesture towards a match official at Deepdale.
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