Fighter of 8-bit Theater does a lot of this, mostly as a side effect of being stupid enough to warp physics. Possibly the best example is when he sees a castle floating in the sky, and declares it to be the invisible sky castle they were looking for.
Black Mage: Does that look like an invisible sky castle? Fighter: Sure, maybe. I've never seen one. Black Mage: Can you imagine why? (long pause as Fighter attempts thought) Fighter: Because they're quite rare? Thief: He's not wrong, you know.
ThisBasic Instructions strip. For added fun, it seems that both of them are missing the point in different ways.
Bittersweet Candy Bowl, Functionally, most of the older students to Tess. Especially Jessica and Rachel, since the lot of them bullying her is a bit hypocritical at best.
Boy Meets Boy: Mikhael decides to use humour to lighten the situation when coming out to his new poker group, by putting down his cards and saying "Y'know, it's funny that I got a straight, because I'm not." Long awkward silence ensues, and Mik figures they're squicked and leaves. We cut back to the group, still sitting in amazement:
"I can't believe he got a straight that early on!" "The man's luck is incredible!" "Guys ... shut up."
In one of their shorts, a man runs over his friend and his reaction is, "OH SHIT! I forgot the ice."
In this edition of Dangerously Chloe, Abby gets very upset to hear that when Chloe has sex with Teddy (Abby's older brother), she will "'love' him to death." Pandora (like Chloe, also a succubus), explains that it's just an expression: "There's very little 'love' involved."
In thisDarths & Droids strip. Jim as Han is desperately trying to think of a way to warm Luke up, and no matter how much the DM emphasises the warmth emanating from the Tauntaun's body, he remains obsessed with using the laser sword to set something on fire. Eventually he decides to they can camp out in the Tauntaun hide overnight ... and he can try to set things on fire again in the morning.
Police Robot: We are being trained as a police force to help solve conflicts among the planet's non-human population. Mayor's Assistant: Our non-human population consists of one person. Sam. Do we really need an entire police force for one alien squid? Police Robot: Sir, I believe if you look past the obvious answer, you'll see one that's even more obvious.
Baron Wulfenbach orders to take Agatha to Castle Wulfenbach and send her back in case she turns out to be useless. His son indicates that "her parents might not like that". Baron replies: "They'll take her back anyway".
Gorb: Vell, letís just keel her. Othar Tryggvassen: Fiends. Kill her and Iíll tell the Baron. Gorb: Vell, mebbe ve keel you, too, shmot guy. Minsk: Gorb... Gorb: Vat?! Minsk: Gorb, dis iz turnink into vun of dose plans... Hyu know Ė de kind vere ve keel everybody dot notices dot veís killin people? Gorb: It is? Minsk: Uh huh. And how does alvays end? Gorb: De dirigible iz in flames, everyboddyz dead aní Iíve lost my hat. Minsk: Dotís right. Und any plan vere you lose your hat iz? Gorb: A bad plan? Minsk: Right again!
Also... when the Baron finds out that the body he just finished regrowing isn't the girl he'd sent Dupree to capture/kill:
Dupree: I saw—she's dead! Baron: You saw what you were supposed to see. You were tricked. She's alive. Dupree:Really?! Baron: Yes. Dupree: But—are you sure? Baron: Yes. Dupree: Wow. She sure looked dead.
Tarvek: If we threw in every minion we have, we might take out one of them. Gil: That's a terrible plan! Minion: Thank you, sir! Gil: There's another twenty of them! We don't have enough minions! Minion: Er...
Black from Grey is... does this from time to time, mainly because he has trouble understanding metaphors ands takes everything literally. For example, when White says that he's pondering the strength of the human heart, Black assumes he's talking about peoples actual hearts and tells him that mending a few cuts doesn't make him a doctor.
The Science Fair arc of Gunnerkrigg Court features two layers of this. Kat's peers (and most of her teachers) focus on the anti-gravity chamber that she invented, completely ignoring the protein crystal growth experiment that was Kat's entire reason for inventing said gravity chamber. And Kat fails to understand why anyone would be more interested in anti-gravity than protein crystals.
In this panel of Homestuck, Jade gives Dave an item that will make his sword able to injure the main Big Bad. The item is a cue ball, but Dave mistakes it for an egg at first. After Jade points out that the item is a cue ball, Dave asks:
Dave:lord english has some sort of severe egg allergy that we are hoping to exploit?
Ben Winchester from Loserz meets and befriends a girl who's much like his old (platonic) friend Jodie — a bisexual girl hot for Anything That Moves. The conclusion he makes... see for yourself here and here.
Misfile: When Ash is having a worse day than usual due to having to go to a gynecologist (which is only a thing because he got hit with a Gender Bender paired with a Cosmic Retcon), Rumisiel, the angel who caused the original problem, walks in. Ash immediately sucker punches him in the gut.
Emily: I think I understand the reasoning behind that, but was it really the right thing to do? Ash:[thinks about it] No. You're right. I should have kicked him in the nads.
In Oglaf, a mugger tries to shake down a traveler.
Mugger: Hey, magical genie here — offering the choice of two wishes! [holds knife close to traveler's face] "I wish I wasn't bleeding through the neck" or "I wish I had my money." Take your time. Traveler:[excitedly] I wish for true love! Mugger: I don't think you understand. Traveler: No! Wait! I wish I could fly!
In another example, when Haley and her rival were forced to go on thieves's guild missions, Haley would remove the pickles from her sandwiches. Her rival assumed that she was PHYSICALLY WEAK to them, and later attacks Haley by pelting her with pickles. It helps that said rival is a complete and total idiot.
Tarquin: At any rate, I'm happy to put at your disposal any or all resources of this kingdom. Elan:(looking at carpet) How do you control it? Tarquin: Fear and intimidation, mostly, though a little torture here and there helps. Elan:(Horrified look) Tarquin: Or did you mean the carpet? Just pull on one of the tassels.
There's a good one in Pacificators. The platoon needed to come up with a way to lure Rendo away from his comrades.
Cinna: (when discussing who would be the best candidate for being The Bait) Hey, what about Ex-Boss [Qamra]? Qamra: Like heíd interested in some one-eyed woman. Cinna: Thatís right, youíre too old.
Pokťmon-X does this when Brendan describes May to Professor Birch, saying that she's 5'4", 100 lbs, brown hair, and then mumbles "nice... firm... breasts..." while drooling (it's a long story, okay?). Professor Birch looks shocked. After Brendan leaves, Birch gets excited... because he thinks May is cooking chicken breasts for dinner.
In Questionable Content, when Dora first sees a shrink, she complains to Faye that they spent the whole session on small talk and never got round to actually discussing her problems. They actually spent it talking about her relationship with her brother, which is one of her issues.
Petey: You want to know what ulterior motive I have for offering your captain and his company a comfortable retirement. Schlock: Yes! You're sneaky that way! Something big is up, and you're trying to manipulate us. Petey: Fine. You won't like the answer, but here it is: I am trying to take a band of career sociopaths out of circulation. [beat] [Schlock draws his plasgun] Schlock: I'm in. Tell me who to shoot. Petey: Apparently I'm sneakier than either of us thought.
Elf: What are you keeping from me! Back-doors sabotage? Para Ventura: What? No. I just don't like being micro-managed. Elf: I can't help it! You're a very small person! Para Ventura: That's not what that word means!
This Schworld History comic has a disturbing example.
The "Cuckolded Husband" storyline in Sexy Losers sees a man repeatedly walk in on his wife having sex with his best friend. He immediately believes their implausible excuse and innocently runs with it until they regret saying anything.
Unwinder's Tall Comics: Director Nathan Blaine makes a sequel to Citizen Kane, named K2: The Death of Kane. There's enough references to the original film's plot and dialogue to prove that Blaine's a big fan of the original Kane... yet somehow he still manages to turn his sequel into a generic action movie with a lot of explosions.
Eli Parker: Anyhow, one of the funny results of this is that Nathan Blaine has clearly, CLEARLY seen Citizen Kane, and he is clearly trying to get everything right, and throw in a lot of references to Kane 1, but he's still completely missing the point. He's a pretty crazy director.
In Voodoo Walrus Grymm is pretty bad about this. But it could just be him being difficult on purpose.
Creepnight: And remember, this time we run a background check. We don't want another basketcase in our lives. Grymm: "I like picnics."
The Whiteboard: When Sandy is railing against "upgrades" done to her car by Doc (which include offensive weaponry) in the September 19, 2012 strip, he insists on pointing out the difference between rockets and missiles (unguided versus guided), a launcher for the latter being what mounted on her car.
In this comic of XKCD, the Alt Text has the character reject the squirrel's advice. Not because the squirrel is obviously a hallucination, but because "What do squirrels know about mental health?"
XKCD also provides another example, that, coincidentally, also focuses on squirrels.