Zack Snyder left the project midway through production after the death of his daughter, and The Avengers’ Joss Whedon stepped in to help overhaul the final cut of the movie.
Zack Snyder remained the credited director on the movie, but numerous reports related to the film have suggested that the movie evolved quite a bit when Whedon stepped in to take the reins.
Justice League is a particularly tricky film to figure out because we still don’t know what director handled what scenes.
Nevertheless, it looks like the scene between Joe Manganiello and Jesse Eisenberg was always intended to be in the final cut of the movie.