This video immediately came to mind when I read that post:direkiller said:getting mewtwo with an ultraball
because my sister used the master ball on a weedle and i did not find out till it was too late
http://www.dorkly.com/video/32627/dorkly-bits-red-wastes-a-masterball
OT: The hardest boss I ever recall fighting was embarrassingly this:

That one boss always pissed me off partly due to the fact it seemed random when he appeared (he suspiciously never appeared when I stocked up on healing items), always destroyed me when I tried fighting him and I could never really grind in the game because my digimon would always kick the bucket before I felt ready for him. I'm sure there were harder fights but piximon was the one encounter I always remember.
Also, I haven't personally fought this but it deserves mention:
