Scenes get left on the cutting room floor all the time. Whether they're removed due to time constraints or simply because someone's acting isn't up to par, it's extremely common to have an abundance of deleted clips following a film's completion. A more recent (and quite perfect example) would be X-Men: Days of Future Past, which not only completely removed poor Anna Paquin from the entirety of the movie, but dedicated its own DVD release to the life-force sucking mutant titled Rogue Cut which featured a whole storyline that never made it to air.
Now, it should come as no surprise that the 141-minute Avengers: Age of Ultron removed some solid superhero moments here and there to make room for... other superhero moments, but it's hard to tell where those deleted scenes would squeeze into the fold. With the MCU 'Phase 2' Box set being released, we're now able to bear witness to a fight scene that takes place after Thor awakens the newly introduced character of Vision. While in the film, things seem to settle down rather quickly, this extra bit reveals the two duking it out for a while before realizing they're actually on the same side.
This battle between friends doesn't stand up to the film's first friendly tussle between Thor, Iron Man, and Cap, so there aren't really any tears shed at Whedon's final decision to omit it. Things are clearly unfinished with things in a pre-edit stage (Tony Stark's chestpiece looks as sturdy as a 7-year old's Halloween costume), but aside from that, everything appears unnecessary. Watch for yourself, and see if the extra minute of fighting would've really made the difference in your eyes.
If it was one more minute of Scarlet Witch, we'd definitely have no objections.