The first and only time I ever over-trained one Pokemon was way back in Blue, when I had a Venusaur before even facing off with Lt. Surge. I hadn't realized what I had done until it was too late. It was only at level thirty-two, so no great tragedy.
I did UNDERtrain a Pokemon, though. In Yellow, everyone on my team was around level forty except for Pikachu. I still don't know how it happened. He was only around level twenty-five, and I almost started crying.
"I'M SO SORRY, PIKACHU!"