***Gold***:
1. Never knew that rugs are doors.
2. Kept training my Porygon while letting it hold the "Up-Grade" hoping that it will evolve, but it didn't cuz you have to trade it HOLDING that item.
3. Killed the shiny red Gyarados, I thought he was some kind of obstacle in the game that I must get rid of to proceed.
4. Teached my starter HM moves, specifically cut & flash, not knowing that they won't be deleted until later in the game.
5. Never knew the Day-Care Center was a "breeding" place for Pokemon. ;)
6. Caught a Pikachu & thought that it would be badass like in the anime...
***Ruby***:
1. Never knew what natures & abilities were, until I was halfway through the game trying to train a jolly Spinda.
2. Thought that the game will be like Gold, you travel to the previous region(s) after the Elite Four, so I held my breath for a Porygon from Kanto's Game Corner.
3. Kept training a Magikarp until it finally became a Gyarados but for some reason it sucked and didn't slay like in Gold.
Too much screw-ups for someone with an internet connection, right? :P