Well I've had a couple bugs while running pokegen, but I can only reproduce one at the moment.
The first, when i was making an absol from scratch I tried to give it bite as its second move. it came up in the program with 0 pp, so i set the pp to the correct number and save the pokemon to my pc. when i loaded the game, the absol didn't have a move in its second slot.
The Egg data for b/w isn't correct. when you modify an egg at all its encounter data changes from the original egg and there's nothing in the program you can do to fix it really.
I've had an issue where sometimes when I set too many pokemon in slots in boxes the program will just hang or crash. I haven't been able to reproduce it today because there's another bug with the same uh.. reproduction steps (which i did record).
This one, when you set too many of the same pokemon into box slots, the program will not let you right click anywhere in the pokemon area. http://dl.dropbox.com/u/1053652/error%201.wmv
Though, even with these bugs I still like this program much more than pokesav.