Went to attack during war and had 3 rage spells available. When I started attack they were not at bottom of page to use. After attack went to check and they were in my spell factory still. Anyone else ever seen this happen?
Did you try to close Clash of Clans and enter it again? Or did you just go ahead and attack? This could have happened to other players too, so I'd take a guess and say it's a glitch, I've experienced this during war four times.
If this happens again, try to close CoC and enter it again as I mentioned above. If that doesn't work, make a post on Supercell's forum page.