Ue o Muite Arukō - better known by it’s English name Sukiyaki - sounds like a bouncy, happy song, but the lyrics are pretty dark. The songwriter had just left a protest in Japan and was feeling despondent and bereft about negotiations between the US and Japan. He talks of looking up while he walks so his tears don’t fall. The English lyrics as recorded by A Taste of Honey had no resemblance to the original.
Paul McCartney once said in an interview about his song, “Blackbird” - “you know, it isn’t actually about a bird.”
Ozzy Osbourne’s No More Tears sounds like a breakup song, but it’s something more sinister. The narrator had actually been stalking his victim, captured her and killed her. He’s saying good bye to her corpse.
It’s steeped in bitter irony, but just reading the lyrics of the chorus tells you to go ahead and do whatever you want because there won’t be any resurrection on Judgement Day. Still a weird song for kids.
See also: Nathaniel Rateliff & The Night Sweats - S.O.B.
Reading the lyrics to all the verses of You Are My Sunshine reveals it to be not quite as jolly as you might think.
Several of the Eagles hits reflect annoyance towards women.
It’s obvious if the listener pays attention and hears the lyrics. But most fans only hear the fantastic vocal harmonies and instruments.
Heck, parents thought they were the clean cut, nice band. Compared to Black Sabbath, Rolling Stones etc. When actually The Eagles were known for trashing hotel rooms and drugs.
Lyin Eyes is just one example. Probably the most obvious anger about a failing relationship.
To be fair, this could apply to anyone in a relationship unequally based on fame and wealth. A Man or woman can see an opportunity to grab what they can.
Peaceful Feeling
Take It Easy
Lyle Lovett does this often. “Nobody Knows Me” sounds like it’s a Romantic look at the singer’s lover, but turns into a song about how he cheated on her and how she knows he’d do it again.
His “LA County” sounds like a song about a friend but is revealed to be about a psychopath shooting his ex at the altar when she married someone else.
“I Married Her just Because she Looks Like You” completely contradicts the message in the title and chorus.
(Lovett was doing a live request show when someone requested it, saying they played it at their wedding (!). Lyle asked if she knew what the song was about. “We changed the lyrics.”)
Mose Allison 's “Parchman Farm” sounds like a man complaining he’s been unjustly sent to prison until the final line “and all I did was kill my wife.”
We’ve done this before, multiple times… I disagree completely. I mean, sure, there is a way to read whatever you want to into the lyrics, but it’s nowhere near the clear-cut „bad“ness of Every Breath You Take or Born In The USA.
In my mind, the singer of More Than Words says „Don’t tell me you love me, show me“, which is not completely unreasonable.
I don’t see how those sound one way on the surface but are really something else - you don’t have to listen carefully to “Lyin Eyes” to figure out what it’s about and there’s not a disconnect between the music and the lyrics like “ Born in the USA” - people only think that’s a patriotic song because the don’t know the lyrics except for the chorus and and the music sounds celebratory.
Third Eye Blind’s “Semi-Charmed Life” sounds awfully peppy and upbeat for a song about struggling with meth addiction.
(Disney even used the “doot-doot-doot” intro in its trailer for The Tigger Movie.)
In a similar vein (heh), the La’s ‘There She Goes’ (more famously covered by Sixpence None the Richer) sounds like an upbeat, romantic love song, but is widely believed to be about heroin:
There she goes…
…
Racing through my brain
…
Pulsing through my vein
…
No one else could heal my pain
And then there are several songs that sound like romantic love songs, but are actually odes to beloved dogs. Barry Manilow’s song ‘Mandy’ being about a dog is supposedly an urban legend, but the Beatles’ ‘Martha My Dear’ and Led Zeppelin’s ‘Bron-Y-Aur Stomp’ are actually about dogs.
As well as “Shannon,” by Henry Gross; it’s a sad song about someone who’s passed away, but that someone is a dog: specifically, a dog named Shannon, who was owned by Carl Wilson of the Beach Boys.
“Last Kiss” is awfully peppy and upbeat for a song about a guy whose girlfriend dies in a horrific car accident.
Pearl Jam’s cover at least slows it down, but the big hit 60s version by J. Frank Wilson and the Cavaliers sounds like a fun, catchy pop song, until you listen to the lyrics.
Likewise, Puff the Magic Dragon. Setting aside any “it’s drugs, man” interpretations, it’s pretty dire at the end. I was once singing it in the shower as my wife was getting ready in the bathroom and she accused me of making up the final verse 
Blondie’s “One Way Or Another” is a jaunty song sung from the perspective of a stalker, based on Debbie Harry’s actual experience with a stalker.
Dave Matthews Band’s “Crash Into Me” is about a peeping tom, and Sarah McLachlan’s “Posession” (kiss you so hard, I’ll take your breath away) is about letters from deranged fans. Both seem to be love songs.
Mention of “Into the Night” by Benny Mardones inspired me to listen to that song again. I’d practically forgotten about it. I’ve always found the song to be a little creepy and I played it many times on the radio. I must admit, though, that it’s one of my guilty pleasures. The over-the-top performance and production is Pop perfection.
I never related it to Benny Mardones specifically as the protagonist, though. Had the opening line made her 18 years old instead of 16 it probably wouldn’t bother me. It could just as easily been about a 19-year-old guy and a 16-year-old girl. A three-year age gap is huge when you’re that age.
When I was a kid, I thought Peter Gabriel’s “Solsbury Hill” was about the rapture (“grab your things, I’ve come to take you home”). It’s actually about his coming to the decision to leave Genesis.
Similarly, the Pretenders’ “Tattooed Love Boys” is a snarling, rocking song, with lyrics that seemingly come from the viewpoint of a flirtatious woman. In reality, Chrissie Hynde wrote it about an incident in which she had been gang-raped by a motorcycle gang.
The Beatles song “Norwegian Wood” sounds peppy and folky, but it’s about a guy who goes to a woman’s house hoping to have sex with her, and you can make a decent argument that he burns the woman’s house down when she refused to sleep with him.