Yes. I lost all my Pokemon in my Pokemon Red cartridge once, along with my save data and ability to save. The thief was a certain game called Pokemon Stadium, and its evil sidekick, the Transfer Pack. There was a bad connection error, and it corrupted my data, wiped the cartridge, and made the game incapable of saving. Plus, just to add insult to injury, the Pokemon Stadium cartridge was wiped of data as well. I lost 6 good Level 100's from that game, and had to buy a new copy of Pokemon Red.
Of course, that could have also been the internal battery dying, but the fact that it happened right when there was a connection error brings up the suspicion.
Since then, I never put any of my games near Transfer Packs, let alone into them, nor do I let anyone else play any of my Pokemon games.