I'd say Waterworld is a good example.
Beat me to it. Stories of a storm destroying a set and Costner sinking $25 million USD into it to keep it afloat made this project more famous than the movie itself.
Ghost Rider is a personal sore point for me. It should have rocked, but it was just wrong!
Alien³ was famously troubled from concept to execution.
King Kong (2005) had clumsiness throughout. Plot decisions created pacing problems and even the 35mm film prints had reel joins mid-scene!!! W - T - F... Okay, so not exactly a complete face-plant, but should have been better.
Perfect Creature. There's a reason why this name doesn't ring any bells. And it's not because they cut my scene either.

Spider-Man 3. There, I said it. The idea had promise right up until some knucklehead thought Venom would be a good idea. Even then, the non-Venom content was pretty crappy and when your hero becomes an ******** performing Flashdance in the street, your movie could well have problems beyond studio interference.
Doctor Who (1996), need a better sonic screwdriver to switch it on.
What Becomes of the Broken Hearted? (1999), the little-known sequel to Once Were Warriors. Actually, maybe a sequel was a bad idea in the first place.
Terminator 3. Terribad. When the director abandons the road metaphor and the survival-of-life themes for a plotless collection of action scenes, then the director has failed to even see the target.
Time to stop before the list gets depressing.