Acclaimed Flop: Major example - it won the Palme d'Or but couldn't make back its own (admittedly large) budget. Only in the home market though; the worldwide theatrical run did eventually make a profit.
Development Hell: Malick began work on a project enigmatically entitled Q before making The Thin Red Line, only for it to come to a halt. Apparently, Malick used Q as a basis for The Tree of Life, which was finally officially announced in 2005, only to have casting issues, gathering up a Dream Team of visual effects artists to achieve his vision, and then work very, very slowly to make everything as good as possible. In short, he's a perfectionist.
Stunt Casting: Sean Penn as a guy with about 10-or-less non-consecutive minutes of screen time and barely one line of dialogue in an over-2-hour movie. Penn has gone on record saying that his role in the final cut contributed nothing to the film and served no purpose; he also mentioned that, in light of this, he was at a loss as to why the director didn't cut him out altogether.
Heath Ledger was originally cast as Mr. O'Brien, and his death put the production into a tailspin before Brad Pitt volunteered to take the part.
The original cut was said to be over 4 hours long, and Adult Jack (Sean Penn) had a much, much larger role. Penn can barely even relate the script he read and the cut they released to be the same movie.
Write What You Know: Malick grew up in Waco, Texas which is where the film is set. Like Mr. O'Brien, Malick's father gave up on his aspirations of becoming a musician but played the organ at his church. Also, Malick's brother died (suicide) when he was a young man, much like Jack's brother R.L. His other brother was badly burned in a car accident, which may have inspired the badly burned neighborhood boy.