The titular character from Crayon Shin-chan does this a lot. Such as saying "Welcome home" when he comes home and "I'm leaving" when someone else comes back. In the gag dub, when Georgie asks Shin if his mother goes to any drunken sex parties he mixes it up by replying that he doesn't know if she goes to any drunken insect parties.
Haruka Suzushiro often had to be corrected by Yukino Kikukawa. In My-Otome, Yukino Chrysant, now a president of a republic, carried a megaphone for the sole purpose of correcting the malapropisms of her Otome, Haruka Armitage.
Sara Gallagher, first of the Five Columns, also gets in on this from time to time.
Haruka: All right, it's show time! We'll destroy this median! Yukino: It's "meteoroid—" [interrupted by Sara] Sara: It's "meteroid", Haruka-onee-sama. You're the mission leader, so please act like one.
Angol Moa from Sgt. Frog tends to punctuate her sentences with "Teyuuka", which is usually "translated" as "It's like…" or "You could say...", followed by a Japanese idiom that's almost, but not quite, appropriate to the situation.
Hermes of Kino's Journey occasionally mixes up his "idioms".
Azumanga Daioh: In addition to her Kansai accent, Ayumu "Osaka" Kasuga has a tendency toward amusing mispronunciation and vocabulary confusion, especially of any non-Japanese words.
Yotsuba from Yotsuba&! mangles words and creates portmanteau words like "Yotsubox" for "Yotsuba's box" — just as you'd expect from a five-year-old.
Tsukasa Domyoji in all versions of Boys over Flowers. In the manga, other characters have even broken the fourth wall to point out his inability to speak certain simple words in Kanji (as represented in his speech bubble).
Dan from Basquash!! has an amazing tendency to mispronounce the names of people and places. He easily crosses into Accidental Misnaming territory with several characters because of this.
Eve from NEEDLESS does this a LOT - though in her case she not only mangles speech, but renames characters on a whim, often with arguments from the victim. Hilarity Ensues. She does this so often that other characters eventually start using the alternate names, the victim eventually just accepts it as a nickname.
The Medicine Seller from Mononoke does a malapropism in the 6th episode by mixing up two different Japanese idioms. Justified in that it's more than a bit apparent he's Not Quite Human.
Bankotsu from Inuyasha is a rare villainous example. One of his first scenes has him messing up the kanji he's supposed to write in a letter to an old enemy several times, and he ultimately has to ask The Evil Genius from his group for help.
At one point in Ah! My Goddess, Skuld is attempting to purchase a mannequin from a store. She offers all the money she has, and says that if it's not enough she'll sell her body. Cue shocked silence from all involved (Skuld appears to be a little girl, after all) until her older sister Belldandy informs her that the proper saying is "I'll work it off."
Yamagata in the AKIRA manga can't seem to contain his "indigestion" note "indignation" and finds no problem "discussing" it loudly.
Non-spoken example: Tomokane from GA: Geijutsuka Art Design Class has a hard time reading and writing kanji. So when the art stream curriculum included typography...
Some of Shampoo's speech from Ranma ½ one notable example "Why you have to be such a sexy pig?!" (she meant sexist pig).
Luffy tends to do this with some frequency. Though this is differently translated between the manga and anime: for example when Kaya gives them the Going Merry, Luffy says "Wow, you're sure adding injury to insult, Miss Kaya!" in the manga and in the anime says "It leaves nothing to be tired." Zoro immediately corrects him ("[Try adding icing to the cake]/[That's nothing to be desired] moron.").
Another example his when Luffy sees Bellemere's grave and says "condolences" incorrectly several times before the mayor helps him out. This situation was a little different in that Luffy can tell that he is saying the wrong word to some degree.
He also remarks, in one episode of the anime, "That's my polisuu!" Sanji then replies "What the heck is a polisuu? You mean policy (same word in Japanese as it is in English), don't you?"
Franky tends to mishear any similar enough word as Hentai/Pervert, and ask if the speaker is talking to him.
Some of Franky's underlings walk around Water 7, announcing that they've captured Usoppnote Not only do they not know that he's left the crew, but they also don't know that Franky was so moved by Usopp's devotion to the Going Merry that he isn't treating Usopp like a hostage at all while demanding that Luffy show himself if he doesn't want Usopp to come to harm. Unfortunately, one Franky Family member gets the words wrong("If you don't want us to think you like emotion" as opposed to "If you don't want us to sink him in the ocean."), resulting in the threat coming off as more comedic than intimidating.
In Yu-Gi-Oh! 5Ds, Yusei adjusts Rua and Ruka's adult-sized duel disks to fit their tiny arms. Amazed, Rua thanks him for "cutmonsizing" their duel disks, then Ruka says the right word is "customizing".
Shino from Seitokai Yakuindomo will occasionally blurt out really obscene things that sound similar to more innocuous phrases, such as saying kinbaku (rope bondage) when she's talking about the Kinkaku temple. Given her personality, it's difficult to tell if she does it on purpose.
Monster Musume: When the police and Ms. Smith are looking for her to have her returned to her host family or deported, Papi tries to explain her situation to Kimihito. Unfortunately, instead of saying "deported," she says "deflowered" (according to the fan manga translation), "aborted" (according to the official manga translation), or "incest" (according to the anime translation).
