Recently I purchased a DVD copy of the 1981 spoof “Zorro the Gay Blade”. If you’ve never seen it, it has no nudity/sexual content and the strongest language is a couple of uses of “shit”. So imagine my surprise when I notice a big logo on the cover stating “M:Recommended for mature audiences”. What other movies/TV shows/albums have warnings or ratings that don’t match the actual contents at all?
Despite being a hard PG/soft PG-13 in all other respects, Planes Trains & Automobiles was rated R solely due to a single (hilarious) scene where Steve Martin says the F-word 18 times in a row.
Well, it does have the word “gay” in the title. 
One thing that struck me as odd is that the MPAA hasn’t used the “M” rating since 1970. I looked up the movie on Amazon, and found copies with the “M” rating. They’re Australian. In the U.S. the movie was rated “PG.”
The Australian rating system is described here. From your description of the movie, it sounds like “PG” would have been a better fit. Who knows, maybe the gay theme upset the censors.
And more recently was the controversy with the rating for The King’s Speech thanks to a similar scene.
Sometimes movies will do something to UP their rating so that adults don’t think it’s a kids movie. Assuming, without that one scene it truly would have been a PG or PG-13 movie, they may have done that on purpose.
There’s a movie called Whale Rider that’s generally about as family-safe as you can get, yet has a PG-13 rating, due to one scene that features some of the adults smoking marijuana.
And if memory serves, there was a pretty clear “substance abuse is bad” vibe to it, too.
On the flip-side, Poltergeist was somehow rated PG and not R. I have heard that backlash about the low rating motivated the creation of PG-13.
This is true, but it’s typically done to avoid a G-rating (I believe Searching for Bobby Fischer deliberately inserted a few swear words to get rated PG.) Most movies will do their best to avoid an R-rating, especially a family-friendly John Hughes film.
Similarly, Stand by Me was rated R solely for language.
That one, and Indiana Jones & the Temple of Doom (in which an Evil Thugee RIPS A MAN’S HEART FROM HIS CHEST AND SHOWS IT TO HIM BEFORE HE DIES) was the primary impetus behind establishing the PG-13 rating.