After reading through all these Master Ball stories, here's mine: In Pokemon Emerald, in one of my first playthroughs, I threw my Master Ball at a Level 30 Wingull because it knew Quick Attack. Seriously. Also, I just found a very old Fire Red cartridge that I thought didn't even work, and I found my team to be: A level 64 Charizard with Blast Burn, Metal Claw, Flamethower and some other Fire-type move; level 50 Articuno caught in a Master Ball (JESUS), with three of its original moves and Fly, level 28 Hitmonchan with only the elemental punches, and a level 38-ish Nidoking with HM slave moves. I remember this savefile and on it I've yet to beat the Pokemon League. I don't even know how I'll do it but ok lmao
Ok I remembered another one: In my Pearl savefile, a Bad Egg showed up once. I had absolutely zero idea what that was and before looking it up on the Internet (cut me some slack people this was 2010 ok lol) I decided to try and hatch it (failed) and ask my cousin (who I thought was this sort of Pokeguru because 9-year-old me lmao). Turns out he was a jerk and told me it was because I had three shinies from different games, which caused a 'Bad Virus' to show up in my game in the form of that Bad Egg, and that if I didn't do something my console would blow up (I WAS REALLY GULLIBLE OK?). So scared little me asked him what did I have to do, and of course the answer was that I had to 1) give him all my shinies (a collection of my shinies from various games too ;-;) 2) delete my savefile (with hours of time on it and even event Pokemon) and 3) release all Pokemon that came from that file and were in other games (hint: a lot)... I still cry internally when I remember that. I'll always remember you Member's Card Darkrai from Pokemon Platinum... At least I can do the tweaking glitch and catch one or inject a Wondercard on my savefile...