There are many more than three, and you will discover this in the sequence in the Whirlwind Maze at the Northern Crater. You see a large procession of Sephiroth clones snaking their way up the mountainside towards the centre, some of them fall off along the way. I don't know if this includes the ones seen in Nibelheim previously, but there are definately more than three. This doesn't, of course, include (SPOILER)Cloud.