Director Doug Liman ("The Bourne Identity") and Jolie ("Tomb Raider") had a major fall-out during the course of filming, reported imdb.com.
Insiders insisted that both the actors were consummate professionals on the set and that their real concern was how badly the film might do because of the fall-out between the director and Jolie.
"You can tell when people are messing around, and they weren't. If they had an affair, it was well hidden," a source told British magazine OK!
Pitt, 46, and Jolie, 29, are rumoured to have had an affair during the film shoot last year, which led to the recent split between the "Troy" star and wife Jennifer Aniston.