This is my brother’s favorite:
Lois Lane: So, how did you enjoy your first day on the job?
Clark Kent: Frankly, the hours were somewhat longer than I expected, but meeting you and Jimmy and Mr. White on the whole, I think it’s just sweat.
Lois Lane: “Sweat”? You know, Clark, there are very few people left in the world these days who sound comfortable saying that word.
Clark Kent: What word?
Lois Lane: “Sweat”.
Clark Kent: Really? It just sort of comes naturally to me
As I recall, the word in the scene is ‘swell,’ not ‘sweat.’
Sounds like the brother is the one who misunderstood. 
No, it was me, but he was the one who found it funny.
Not a movie but a TV show: “There’s always money in the banana stand.”
Trisha’s not comfortable using that word…
You can’t fool me. There ain’t no sanity clause.
Nothing beats the one in Frasier when the ice sculpture at Marty’s wedding was melting:
FRASIER: (In a panic) My Balzac is dripping!
ROZ: Don’t worry. In those dark pants, no one will ever know.
Dorothy and the Scarecrow have found the Tin Woodman and are trying to understand what he’s saying:
Dorothy: He said “oil can!”
Scarecrow: Oil can what?
Probably because I was watching without my contacts in, I totally missed the joke in the episode of Big Bang Theory where Sheldon goes crazy trying to figure out Howard’s card trick. I had to see it three times before I got that Raj was Howard’s stooge (he lied about all the cards he drew from the pack, and flashed him a signal when Sheldon did it), and that Penny was in on the scam.
I meant your own misunderstanding.
There were a couple in Wayne’s World (it came out the end of my freshman year in high school, so it was huge to us back then)…
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The “No Stairway to Heaven” gag. (I didn’t see this part until it came out on videotape, so of course I got the redubbed version. Also I hadn’t actually heard the song “Stairway to Heaven” at that point in my life, and of course knew nothing about the actual ban on playing “Stairway to Heaven” in guitar stores.)
What I got out of that scene was, it looked like the “No Stairway to Heaven” sign was posted above a doorway, so I was thinking, “Is there an actual stairway behind that doorway? Where does it actually lead? Do customers think it leads to heaven and try to get up in there, but it only goes up to an office or something, and the clerks got tired of shooing everyone away so they put up that sign?” -
The scene where Wayne and Cassandra were having a conversation in Cantonese (with English subtitles), and Wayne makes a very short comment. At least it’s short orally. The subtitles take about 20 to 30 seconds to cycle through, while Wayne just sits there looking bored. At the time, I didn’t get the point of the joke (a long thought that takes almost no time to express orally), and thought that was just Wayne’s internal monologue being subtitled.
Not sure if that’s what the OP meant by “misunderstandings”, but there you go.
I always heard the “Can you even dye my eyes to match my gown” line in the Wizard of Oz song was “Can you even dye my eyes to match my dog.”
In my defense, it kinda sounds like that (the pronunciation of “gown” is more like “gahn” with the same vowel sound I’d use in “dog”), and she is holding Toto at the time, and dying ones eyes to match something is kind of nonsensical to start with.
I did catch the signal at the end but didn’t understand what was going on until then. It did strike me as being well written. That would be the perfect method to fool Sheldon and drive him crazy
I enjoyed reading these responses.
My second favorite misunderstanding was when Hermione said the “library for a bit of light reading” I thought she said “library forbidded light reading” and I used to think light reading meant using a lantern to read in the dark. Then when Ron said “This is light” I thought he was stating that there is light because it was daytime so there was no need for a lantern.
At one point in the middle of the episode, you can actually see over Raj’s shoulder which card he’s holding, and he lies about it. That’s the tipoff the whole thing is a scam.