Do you mean fighting against each other?
Because if so, the answer is no. They have always been pretty good friends. I mean sure like any good friendship there are disagreements, but they have never gone as far to shoot a bullet. If I recall there as been 1 or 2 punches thrown when Castle was drunk, aside from that nothing.
'In the 1995 "Over the Edge" crossover, the Punisher is captured and sent to a maximum-security facility with a S.H.I.E.L.D. escort. During a hypnosis session with Doc Samson, Spook interrupts and has the Punisher conditioned to believe that Nick Fury was responsible for his family's murder. He escapes the facility after a Mafia attack and goes after Fury. At the climax of the storyline, the Punisher kills Nick Fury, who was buried at Arlington National Cemetery.
However, in the Fury/Agent 13 two-issue limited series, it is revealed/retconned that the Nick Fury that the Punisher "killed" was a highly-advanced Life Model Decoy designed by Tony Stark (Iron Man), and that Fury was never dead.'
