No truly interesting movie can be subject to a single interpretation—even if the writer and director say it’s about one thing, some viewers may have a different take. That said, here are the movies that most would agree have been misunderstood throughout the years.
I think in general any time someone makes a movie criticising some idea by satirizing what that idea looks like when taken seriously, some percentage of people will miss that it's satire and just think it's seriously advocating that idea. For example starship troopers is a fantastic movie and a great critique of militarism using satire. But a decent chunk of people watch it and think it is unironically glorifying militarism.
I would add "Crouching Tiger Hidden Dragon" to this. Everyone I know recalls that movie as: "They could all fly, and in the end, she flew away off the bridge to live happily ever after".
I interpreted the movie as a total tragedy of the main character's life, and, in the end, she jumps from the bridge to commit suicide.