Dawson Casting: Then 37-year old Warren Oates played O.W. Hadley, who is referred to as a "boy" despite the fact that he's clearly anything but (he was actually two years older than Richard Harris, who played his Confederate commanding officer). Borders on Narm when he dies and everyone continually refers to him as a "boy" despite the fact that he was clearly in his late 30s.
Executive Meddling: A legendarily notorious example in the annals of Hollywood, studio heads at Columbia abruptly cut short the film's shooting schedule and kept reducing the running time from over four hours to 156 minutes, 136 minutes at its initial release, and finally 123 minutes. As might be expected, director Sam Peckinpah wasn't pleased with these changes. Supposedly The Wild Bunch was his attempt at a semi-remake. According to star Charlton Heston the film suffered a lot of this (see What Could Have Been below). Among other problems Heston cited that Major Dundee began filming without a properly finished script and that none of the major parties involved had agreed on what the film was truly supposed to be: Heston said he saw the film as being about life after the Civil War, the studio just wanted a standard issue "Cavalry Vs. Indians" picture and Peckinpah, according to Heston, saw it as The Wild Bunch, which would become his most famous and iconic film a few years later.
Troubled Production: In addition to Peckinpah's constant battles with the studio over the film's shooting schedule, budget, content, and length, the director often antagonzied the crew and the cast to the point that Heston allegedly threatened him with a saber. Peckinpah's drinking benders didn't help things either.
By the end, after Columbia had shortened the production schedule because of concerns over this, Heston was reportedly more or less directing the film since Peckinpah often wandered away from the set in a drunken haze. Heston kept Columbia from firing him only by agreeing to completely forego his salary (a very rare move by an actor).
And then Columbia decided to more or less break its contract and edit the film itself instead of leaving it to Peckinpah. A cut close to what he wanted to do wasn't released until 2005, and even then it's largely guesswork.
There were also reports that Charlton Heston and Richard Harris did not get along during filming, much like their characters - even more so that Harris simply did not get along with anyone due to his own real life rebellious nature and "alpha dog" persona as described by leading lady Senta Berger. So great was the disunity between them that Harris would jack up his boots so that he wouldn't look shorter than Heston (which he was, if not by much). Heston joked in his autobiography In The Arena that the reason he and Harris didn't get along was that Harris was an Irishman while Heston himself was of Anglo-Scot descent - while still insisting that things weren't as bad as reported.
On top of all that, at one point Peckinpah's obnoxious behavior angered the normally even keeled Heston so badly when he lashed out at Heston over a shot of the group riding against a blood red sunset that Heston whipped out his cavalry saber and charged at Peckinpah on horseback. A frightened Peckinpah jumped into a boom mic operator's chair and yelled to be pulled up just in time to avoid being run over.
What Could Have Been: Reportedly the film was originally intended to be four hours long, described as a kind of "Moby Dick In The Old West" with Dundee as Captain Ahab and the Apache as the collective whale, but countless scenes went un-filmed due to Executive Meddling.
Legendary Hollywood western director John Ford was offered the chance to direct the film before Sam Peckinpah got involved, but he was busy with other projects and at any rate he just wasn't interested.