Well it does take Sora time to unlock Sephiroth, to be able to fight him. Maybe Cloud had to do the same, or maybe he just had no idea that Sephiroth was there, and didnt know until Sora fought him. Or perhaps he knew, but knew he wasnt strong enough to battle him, especially with the way Sora was kicking Cloud's butt. So he had to wait until he was strong enough before he confronted Sephiroth.