The games are aimed at kids aged 8 to 12, with specific games for third-, fourth-, fifth- and sixth-graders (having been a follow-up to Reader Rabbit, another Learning Company series, which is aimed at kids aged up to 7). In addition, there are four other games devoted to mathematics, language arts, logic and miscellaneous subjects.
Aliens Speaking English: Several times over, both with aliens proper and with other things. Partially averted in 5th Grade—the aliens use Black Speech, the written form of which is a Cipher Language, but their computer speaks and understands English perfectly well.
Closed Circle: 5th Grade, 6th Grade, The Incredible Toy Store Adventure and Reading have game-wide examples. 5th Grade deserves special notice in that everyone on the island is trapped, having tried and failed to get off for generations—they say it doesn't want them to leave.
Wikipedia describes him as Asian, which isn't incongruous with his last name and how he's drawn, but this was never really confirmed in-game.
Gaia's Vengeance: 6th Grade's plot comes about because of waste dumped in the water supply.
Generation Xerox: The apparent reason why the human residents of the island in Grade 5 still act and dress like they're from the time periods when their ancestors wound up there.
Gentleman Thief: Crime has caught up with the one in Grade 5's game; he's in a stockade. He buried a lot of cryptiles in a patch of Man Eating Plants, and given your need is willing to loan you the maps.
God's Hands Are Tied: Of all the series to parody this...Grade 4 introduces Egyptian gods towards the end, who provide the main characters with magical boons to help them defeat Set. Said gods would fight him themselves, but the passage leading to him is marked with a sign: "You must be under this height to defeat the forces of Chaos." (And the height is forty feet, no less!)
Mythology Gag: Upon meeting the sarcastic sphinx, Leslie says, "It seems somewhat odd that we would encounter a character like this in an Ancient Egyptian pyramid." He then replies, "Who were you expecting? Reader Rabbit?"
Obviously Evil: Even without the name, the above-mentioned Alistair Loveless might just as well be walking around under a neon sign reading "BAD GUY".
Humorously enough, even That Other Wiki observes in its article on the game that there's something off about him. "In one scene, he cackled manically for a long time in the typical villain fashion, before coughing and explaining that he swallowed his mint."
Omnicidal Maniac: Malicia in Reading. As you might expect, she's completely bonkers.
Series Continuity Error: In Mystery Mansion Arcade, when Miss Rose is revealed to be one of the villains that have captured the team, Joni makes a comment about how "the pollution must have made you evil again". All well and good and a perfectly reasonable explanation. Problem? Joni is the only Clue Finder who doesn't remember the events of 6th Grade Adventures where the character was introduced along with the pollution issues. Though this could be justified by Joni being the only person the other three told.
Tech Marches On: The kids keep in contact with each other using "videophones" invented by Santiago. At the time the games were made, commercial camera phone did not exist in North America and regular cell phones were not widely used by children anyway.
The vending machine in Search and Solve and the Gates in Reading. This is actually the entire point; it's to test out your hypothesis. This doesn't stop it from being frustrating for people of any age.
Those who had played games like Mastermind or Lingo would be will familiar with the gates challenge in reading...however, you have to GUESS what letters are in the correct or incorrect places, since like Mastermind, you're told how many letters are correct and are in the right/wrong spaces, but you aren't told which ones.
The gate challenges in 3rd Grade's Monkey Kingdom are very much like this especially on CHALLENGE difficulty. Oftentimes the appropriate addition, subtraction, multiplication AND division tiles will all be visible and you just stand there throwing sneezeberries at them hoping that they're correct. But once you know where the letters are, you can just hit them, even if the numbers don't match up.
Unwinnable by Design: The mentioned Trial-and-Error Gameplay mini-games can be made unwinnable. If the jams in the vending machine puzzle are clustered to one area and your guesses are all on the other side...you run out of guesses and can't win that game. In the gates challenge, you can easily run out of guesses considering you know how many letters are in the right or wrong places...but you don't know which ones they are.
Weirdness Magnet: These kids can't even go out into their backyards without finding trouble.
Malicia in Reading tricked Joni and Owen into assembling the Amulet of Life for her, then when she tried to grab the completed amulet from them, got the wrong one, but she fortunately already had Leslie and Santiago imprisoned in her mountain so naturally, Joni and Owen would walk right on up and bring the amulet to her anyways to rescue their friends.
The Big Bad of Mystery Mansion Arcade also has this, where the mysterious villain, none other than Carmen Sandiego who has organized it all traps the villains after they fail, and the kids even ask, "Wait, did she want to catch us, or them?