Goofy asking what an airport and a digital clock are in the flashbacks of the short "Hickory Dickory Mickey" may at first be him being his usual dim-witted self, but said flashbacks are styled after the original black-and-white Mickey Mouse cartoons, which were made long before digital clocks were even invented and when airports (and aviation in general) were still very much a "new" thing.
How did Goofy figure out that Pete wasn't Snow White in "Pluto Saves the Day"? Because he waits the tables, so he knows where she sits!
It's tough to see Panchito without his pistols and Jose without his cigar, but they're indoors, in the early 2000s. It's not unlikely that the House of Mouse has a no guns, no smoking policy. Given that villains are guests, the no weapons policy makes sense. And Jose probably takes smoke breaks outside with Basil, Cruella De Vil, and the Caterpillar.
Addressed in the pilot, where Mickey goes over the policies: "No smoking, no villainous schemes, and no guests eating other guests"
The Queen of Hearts rejecting Mortimer in the Valentine's Day special—while everyone was rejecting Mortimer's advances, the Queen of Hearts is also married to the King of Hearts (who cameos at the end of the episode even), giving her an even more legitimate reason to be angry at him for trying to flirt with her.
In "Pete's One Man Show", after all the guests scram upon being told Pete's going to do a show, Mickey and the gang have to hide behind cardboard cut-outs of the Disney characters and speak their catchphrases (and of course, Goofy hides behind Dumbo's cut-out and says "Be our guest, be our guest!"). Most likely, a Self-Deprecation on Disney's part about criticism of most of the characters being in episodes to say their famous lines or recreate their famous scenes.
The song "My Name is Panchito" reveals that several of Panchito's relatives ended up as drumsticks. No wonder he's so insane. He doesn't seem too cut up about it, but is that because he's a rooster and has the attention span of one, or because he has taken refuge in madness?
In "Suddenly Hades," Pete breaks the air conditioning on a day so hot that only Hades remains in the House of Mouse. But the guests regularly include characters from "The Lion King," "Tarzan," "Aladdin" and "The Jungle Book." It was so hot that people and animals from the blazing deserts and steaming jungles couldn't handle it!
The implications of the short "Topsy Turvy Town" can easily become terrifying through some Fridge Logic. If people who were arrested for breaking the law are actually rewarded through their punishment, by logic, those who respected the law are punished for real. And I'm not done yet: the greater the crime, the greater the reward, which means those inmates who Mickey and Minnie found in the dungeon were actually people who did great things for Topsy Turvy Town and got severely punished for it.
