Walsall won the game 2-1 to book a third round tie at either Charlton or Stockport.
But there were ugly scenes at the end of the games near the visiting fans enclosure, with most of the players from both teams involved.
Carlisle manager Paul Simpson claimed after the game midfielder Jamie Devitt was punched and left with a black eye and that a Walsall player was to blame for provoking the scenes.
Walsall boss Michael Flynn claimed he saw a Carlisle player throwing punches until the brawl was eventually broken up by stewards and staff.
Reports from Carlisle suggest the matter may be investigated by the Football Association though the governing body is yet to confirm that.