Chapter 53 of Attack on Titan has everyone worrying about how Eren can't harden. They're referring to his Titan form's crystallization ability, yes, but it's not hard to misinterpret.
The theme song to the first season of Cardfight!! Vanguard is entirely in Gratuitous English, and some of it sounds... strange to native speakers. The following lines are probably supposed to be about the spirit of competition, but that's not what they sound like...
We can't hold back this feeling Just any longer Come on, tear off everything you've got Get crazy way!
It doesn't help that the lyrics are sung over images of Aichi and Kai, two characters with Ho Yay so strong, the series itselflampshades it.
In the season Legion Mate Arc, the word Mate had become this, even to the Australian's standard. It's funny enough to say it to an opposite gender, but it's funnier to say it to another with the samegender.
In Death Note, when Misa meets Light, she tells him "I don't care if all you do is use me," referring to using her as a weapon. Still, that's not the first thing that pops into anyone's mind. Given that she later explicitly offers herself sexually to Light (and was stalking his alter ego for months before they met), she may have been talking about sex as well.
Tai from Digimon Adventure is especially guilty of this, particularly because of his tendency to say he needs to "hook up" with the others rather than use the much less sexual sounding "meet up". Examples of this include episode 22, in which he said he needed to "hook up" with the others, and episode 36, in which he told Sora to "hook up" with Matt. Thatdefinitely blew up in his face.
Lancer: "You are as good as naked before my spear."
There's a particular scene in the anime of Fruits Basket where Tohru is sick and Hatori needs to give her an injection of some sort. Shigure makes comments about the size of Hatori's needle, and Momiji says something along the lines of "You have to stop if she says it hurts!" The entire scene is just one giant innuendo.
During Mustang's fight with Lust, he makes a comment/threat about making her go down on her knees.
At one point, Alphonse's armor is temporarily possessed by Pride. The official FUNimation sub has him saying "The homunculus Pride came inside my body," and remarking how it made his soul feel "icky" when he later tells Hohenheim what had happened. It really doesn't help that Pride himself is essentially a tentacle monster. Even more disturbing since Pride takes the form of a child during most of his non-tentacle monster screen time.
Father wants Hohenheim to be part of his body, and is quite aggressive about it.
Edward defeats Pride by transmuting himself as a Philosopher's Stone and "forcing his way inside" Pride. Both Ed and Pride are having an Out-of-Clothes Experience for this scene.
In the English dub of the 2003 anime, there's Al saying that he doesn't remember what Ed's skin feels like, and a line about how Winry should care more about Ed's "human parts". Someone actually asked Vic Mignogna about this line, wondering what Ed meant by his "human parts", to which he replied "What was I thinking? I want to know what YOU were thinking!"
Full Metal Panic! Fumoffu has Tessa (a submarine captain) say she's in the "water business" — which is Japanese slang for prostitution. The English version changed the line to "Getting wet is my business" to preserve the meaning.
The sequel has Andy telling MIX he wants to "Fill her hole." It's actually supposed to be poetical, in that he means the "hole in her heart" which is how he refers to the emotional pain she has from her family issues, which he called a hole in her heart that despite her power to seal open spaces or holes she can't fill herself. MIX of course thinks he's asking her for sex and gets majorly offended.
Batou: "If it looks like you've gone in too deep I'm pulling the plug and taking you home!"
Gigantor: "Dick Strong penetrates deep into the mighty fortress!"
Gunsmith Cats: Rally Vincent had to drive Bean Bandit's car once while sitting in the unconscious Bean's lap. She calls it "The worst ride I've ever had!" Which doesn't mean much from an innuendo perspective, since she's canonically a virgin.
The sword Tetsusaiga from InuYasha is astonishingly phallic. It even throbs with warmth when "awakened" and grows hair on its hilt. The sword is "awakened" by "protecting" a WOMAN. Plus powerful energies being "released" from it.
Oh, don't worry, we love children very much. We'll take good care of you. Heh, heh, heh.
In Naruto Suigetsu once implied that Karin (who has an unhealthy obsession with Sasuke) had previously did... "something" to Sasuke before. Whatever this "something" may be. Like with some of these other examples, it's not certain if this was a genuine accident or more of a case of Getting Crap Past the Radar.
Kimimaro to Juugo:
'Yes. I'm going to absorb the enzyme from your body into my own.
Tobi to Naruto during their fight.
Tobi: I touch you, I win!
In The Last: Naruto The Movie, there is a funny one between Naruto and Hinata. Trying to give her present with an empty stomach, Hinata gets beyond embarrassed when it growls. Naruto tries to be kind to her as always but his choice of words come out quite wrong:
Naruto: There is a cup of ramen in my room, if that's okay.
Oda Nobuna no Yabou: "It's dark and hard... And it's got this gooey white stuff splashed on it..." note this was said by Nobuna regarding Yoshiharu's fried takoyaki. And by fried takoyaki, it means literally fried takoyaki, mind you.
Although, by the look on her face and her voice, it certainly doesn't seem accidental; Innocent Innuendo may be closer.
The contract-making process in Puella Magi Madoka Magica has some of this. Sayaka's is probably the worst offender: she asks Kyubey to "do it," and he sticks his extendable ears inside her, prompting some anguished gasping. Then he tells her to "open yourself and accept it; this is your destiny" as she collapses onto the ground. It's no wonder he's a Memetic Molester.
Saki: If you disregard (or, like Momo, don't know) that Hisa was going to challenge Yumi to a mahjong game, this exchange comes off as it.
Yumi: We got along well last night.
Momo: Last night!? Got along well...!?
Hisa: Let's do it again today.
Interestingly enough, in the manga, while Hisa seems to be intentionally giving Momo that impression, in the Zenkoku-hen version, where only Yumi is telling Momo what happened, it seems to be a combination of less-than-optimal word choice by Yumi and Momo's overactive imagination.
Chapter 6 of Sankarea gives the reader "Please treat my body carefully from now on... Furuya-kun."
In School Rumble, Harima talks about his cousin Itoko to Yakumo and says something like "Of course I love her, she's my cousin". However 'itoko' also means cousin in Japanese, so Yakumo is hearing "I love her, she is MY Itoko". Yakumo is asking why Harima is living in Kusakabe Sensei(Itoko's) house. Harima, being the honest person that he is answered "She is my Itoko". Itoko is the Japanese of cousin. So he basically said "She, is my cousin" or "She is my Itoko". It takes a "What?" and rehearsal to make Yakumo understand the meaning.
In S-CRY-ed Asuka Tachibana tends to talk about his balls a lot. Well, his floating green ones, anyway.
In the beginning of Tokyo Underground, the hero is killed and then revived by the heroine. A massive beam of light is used to indicate his life returning to him. This much is fairly normal; however, the blast of light seems to be emanating from his crotch. Completely unintentional, but hilarious when noticed.
This line said by Zero to Yuuki in chapter 72 of Vampire Knight: "If you don't like my behavior then force me into submission." Though one could question if it was really accidental.
Probably pushing it somewhat, but a lot of fans got a laugh out of chapter 60, where a random guard upon seeing Zero carrying a girl responded with the question "I take it you need a bed?"
Sumire, from Venus Versus Virus, does this a lot. Lines like "I swear I'll never leave your side!" can be taken differently. However, this is a yuri manga so...
In the Yu-Gi-Oh! manga, there is definitely some questionable statements Jounouchi makes to Yuugi. One humorous lampshade example being when Yuugi mentions that their digital pets have the ability to mate and gain strength from each other (which is awkward in the first place) to which Jounouchi responds, "Yuugi and I must mate at once!" Honda comments in frustration that people overhearing might get the wrong idea.
Yu-Gi-Oh! GX: In the original, Edo (having the D-Hero deck), often says things like "the power of the D" or similar in reference to destiny. When "the D" is taken to be the OTHER one, some really hilarious accidents occur.