It might stretch the definition of "great" movies, but let's go there. Sofia Coppola, in The Godfather, Part 3.

"Daaaaaaaad?"

When people cheer at what was supposed to be the most poignant moment of the movie, something's gone horribly, horribly wrong. And the "chemistry" with Andy Garcia's character Vincent was non-existent, making the whole subplot about Vincent having to choose between Mary and his ambitions within the Corleone family pretty laughable. I don't know that a better choice (I think the rumor is Winona Ryder was supposed to get the part and dropped out) would've made TG,P3 a Best Picture candidate, but it might have at least come together as a worthy end to the trilogy instead something fans of the franchise wince at the mention of.