Adaptation Explanation Extrication: The ending is actually set up by a line Polly spoke in the opening exposition, "There's still one more question, the extra credit question and it's super hard. That's why I've been looking for you, Knotley." This was cut in later releases, making Polly's demand at the end of the game that Botley still has to do the extra credit question come out of left field.
Alpha Bitch: Subverted. Being rich, blonde, and snotty, Polly has all the usual indicators. However, a throwaway line from Botley indicates Polly is unpopular at her school.
Continue Your Mission, Dammit!: In educational games like this it's expected for the player to be able to take his/her time, but this game ups the counter-method to extremes. Since Botley is characterized as overreactive, he would chide you if you strayed from his mission path. And if you insisted on straying, then Polly herself would chime in and taunt you that you were looking in the wrong place. But the messages Botley gave for idling too long nearly turned this into Guilt-Based Gaming, ranging from "You're hesitating, is something wrong?" to "Of all the times to freeze on me! WE'RE SOOO CLOSE!" and "Pull yourself together, man! Are you having second thoughts about helping me save the world?" At its worst, he calmly informed you "Look, it's nothing personal, but if you're not up to this, I can always go back to the schoolhouse and find someone else". It comes as a real shocker when your robotic exposition fairy admits to the player he believes he or she is probably broken, but that likely would be the case if you idled so often, probably because the player was too busy listening to the background music to listen to him.
Deus Exit Machina: Polly's father is out and he's apparently the only one who can keep her under control. At the end of the game, he returns home and punishes her.
Botley did mention how he was off to a time traveler's convention, which gives us a reason why Professor Sparks came back as soon as he can.
Fridge Logic: Why doesn't Polly just go back in time and give herself the answers before the quiz rather than going to all the trouble of changing history?
Fridge Brilliance: Because that would create a Grandfather Paradox. If she gave herself the answers and she passed, she would never have gone back in time to give herself the answers. Or she just didn't think of that.
Fetch Quest: 4 items per robot to answer specific questions to where Polly sent a specific robot. Since there are 25 robots, you'll need 100 items.
Insecurity System: The security procedure to open the front door of Mystery Mountain is... literally a game of "Simon". Yeah, brilliant move, Profesor Spark — that'll keep out potential thieves and nosy reporters for sure. Okay, Gameplay and Story Segregation.
Missing Mom: The absence of Polly's mother is never explained.
Plot Coupon: The 25 robot. To get those, you need 4 items to answer the "Who, What, When and Where?" regarding Polly's test questions. In short you'll need 100 items.
Prolonged Prologue: Mostly, it's Botley and Polly going on and on with exposition, with some points needlessly repeated and little to no user interaction. It was edited down in later releases, though this resulted in the Adaptation Explanation Extrication mentioned above. Also, some Back Story information was cut, for anyone who cares about that.
Raygun Gothic: The whole aesthetic of the game's universe. This includes Polly's school, which for some reason is an Art Deco version of an old-fashioned, one-room schoolhouse.
Sinister Surveillance: Polly spends all of the game lounging in a room with monitors which display every room in Mystery Mountain. She communicates with you and Botley through various monitors around the Mountain, never meeting you personally — kind of like Khan.
Villain Ball: Polly hides clues throughout the mansion that you need in order to stop her and even sometimes explains what you need to do to find them.
Well, it's no fun if you can't combat her, she's a kid, she's probably having more fun screwing with Botley than anything else.
Warp Whistle: The report card in the inventory will take the user to any game in the Mansion.