-- Saint Bernard of Clairvaux
This one is a little more vague than the other entries, but it's no less important. The problem with movies being a consumer-driven industry is that, by and large, to get the studio to OK spending the massive amount of money needed to put a visually stunning movie in theaters, you need to appeal to the lowest common denominator. The only other way is to assemble such an overwhelming amount of talent around the project, that the studio believes the individual pieces' built-in audiences will carry it past any financial risk. The issue with the more common method (appealing to the masses) is that these are the same people who drive "American Idol" to #1 in television ratings and make 50 Shades of Grey a bestseller: they are not equipped to identify creative merit. The better angle would be to greenlight the most creative works they can and hope to catch audiences off-guard, but that tactic requires a level of (relative) courage that studio executives don't possess. It's harder to predict, but that approach would raise all boats, so to speak. If audiences could trust studios to churn out quality instead of pandering, they might be willing to take a chance on a movie that looks mediocre.
This is one of the few that can go unnoticed during filming regardless of who's involved. Even amazing movies can have fatal flaws that render their entire story null and void (my personal favorite movie, Inception, should have ended when the van went off the bridge; Arthur was one level down, meaning this would have been his kick, and he would have woken up, leaving nobody to wake the others). Because of how movies are shot by multiple units and out of sequence, some of these plot holes can evade discovery until the final result is put on screens for audiences to pick apart. Sometimes, however, they're the simple result of not fact-checking (the Transformers 3 trailer features astronauts waiting until the moon rotates so they're no longer in contact with Earth to perform their clandestine mission; the moon orbits the Earth with the same side always facing us, like a hammer thrower spinning before releasing the hammer). Either way, it can't completely kill a great movie, but it definitely detracts.
Sometimes you can have a great finished product that you hand over to the studio, only for their marketing department to completely butcher the promotional materials. Another strike against John Carter, this is one that it's hard to blame the actual movie for, but it shows up on the list because it's definitely a mistake specific to certain movies. Alien 3 put out teasers claiming it was bringing Xenomorphs to Earth before setting its movie on a distant space prison. In Bruges had trailers making it look like a Snatch ripoff. I can't imagine the frustration of filmmakers like Steven Soderbergh when he finally sees the trailer for his brilliant Solaris... and watches 1:30 of trying to reduce it to a rich man's Event Horizon. Don't believe the power of trailers? Check out Mrs. Doubtfire recut as a horror movie.
The choice of who to lead productions is a crucial one. Uwe Boll continues to find work despite never scoring higher than 25% on Rotten Tomatoes despite 47 tries. Not every movie can have a top-tier director - there's only so many of them to go around - but every now and then a movie is paired so poorly with one that it should have been obvious to everyone involved what was about to happen. Putting Joel Schumacher in charge of the Batman franchise was so woefully misguided, the damage he would do to the brand name so obvious, that the fact that Batman Begins was ever made is somewhat surprising. People are quick to blame a movie's poor reception on actors trying to play outside their comfort zone (I just did with Psycho) like Jim Carrey in The Number 23 (Hi again, Joel!) or Robin Williams in One Hour Photo, but a director being overwhelmed is just as damaging.
This is arguably the trickiest thing to do right. Your story will end, but the world will keep turning (with rare exception, e.g. Knowing) so your ending needs to be well-defined but account for the fluidity of life. Some filmmakers like Spike Lee never quite get the hang of it, while others like Steven Spielberg have gotten them to an almost too assembly line level of perfection. Twist endings have become cliché, so filmmakers are left with a shrinking toolbox to choose from when trying to leave their audiences impressed when they roll credits. It's easy when doing this to completely lose sight of what the rest of your movie was about; the desire to put a bow on it becomes so strong that you break character just to have a message. Alternately, without an ending in sight during the screenwriting process, they can be muddled messes that don't really feel like an ending. Ending a film ambiguously is one thing, but that's still an ending. Some movies just stop and don't understand the difference.
Plenty of the rest of these entries can be traced to this one. Budget can dictate your casting and crew, and those two elements can control almost the entire rest of the film. This is not to say that all movies should have as much money as they want. Plenty of travesties like Waterworld and John Carter would probably have less vitriol hurled at them if they'd kept their budgets in line. However, plenty of great movies are made when the accountants get out of the way (Avatar, The Lord of the Rings trilogy) and plenty of movies with interesting premises are derailed by low budgets before they ever start shooting (Red Riding Hood, Spawn, In Time).
You'd think this was a foregone conclusion, but alas, movies like Only God Forgives prove that even when the acting, soundtrack, and directing are all spot on, the script is just as essential. Not only the concern of solo screenwriters trying to be progressive, this can be an issue when there are too many cooks in the kitchen. Prometheus began as a straight Alien prequel whose many plot holes aren't present in earlier drafts of the script. Then additional writers were brought in to touch up the script, and we got a movie that wants to be 3 different movies at once.
Of particular disdain amongst filmmakers is the ratings system imposing arbitrary limits on the stories they can tell. Especially notable when studios deign that a director's R-rated creation needs to be edited down to PG-13 to reach a broader audience, this one can absolutely wreck a film. Movies like Live Free or Die Hard and Daredevil have notoriously better scripts that were planned before the powers that be decided to get a piece of those sweet, sweet teenager dollars (with Daredevil having actually shot it and made it available as the vastly superior Director's Cut). Conversely, I Am Legend's original ending completely changes the meaning of the rest of the film along with actually making Robert Neville the villain of the movie. It was seen as too dark by the test audiences and changed to the cookie cutter "noble sacrifice" ending we got in theaters.
Acting is not a skill that can be measured on a linear scale. Brad Pitt couldn't play Wolverine just as Hugh Jackman couldn't play Tyler Durden. Too often, however, movies are guilty of valuing a great name over a great fit. Hey Highlander, you know you're set in Scotland right? So you tried to make Sean Connery play... a Spaniard? From "Bawshelohnuh"? Other offenders include The World is Not Enough (Denise Richards as a nuclear scientist... named Christmas), the remake of Psycho (Vince Vaughn as Bates) and Dracula (Keanu Reeves as Harker). When an actor gets too big to screentest, casting directors can lose sight of the role they're trying to fill. Along the same lines, actors can mail in their performance (Natalie Portman in the Thor movies, or Robert De Niro anytime in the last 10 years comes to mind), dooming what might have been inspired casting if they'd tried.
At last we get to it: the cardinal sin of movies, responsible for many examples of every other entry on this list. Studios are run by businessmen who love to think they're the smartest guys in the room at all times, regardless of the fact that they're not creative in the least. The end result is that they can't get out of their own way on movies. When I did a Throwback on Kingdom of Heaven, I used the Director's Cut, because the theatrical release was incredibly altered by 20th Century Fox, notably cutting 45 minutes from a movie that, when restored, stands alongside Scott's other works admirably. The aforementioned Alien 3 is so notorious for this that the Alien Quadrilogy box set features a documentary of how terrible the production was thanks to studio involvement (Fox again!). Kevin Smith tells a great story about studio interference, this time at Warner Brothers, that even at almost 20 minutes, is a hilarious watch that I highly recommend. It's absolutely fantastic, and I bet it happens in Hollywood a lot more often than people think.