If you're having Giant Eyes spawn inside the stomach (read: where the 2 flesh tentacles are), you are getting a bug.
If you're having Giant Eyes spawn inside C'thun's body (read: in the middle of the thing that you are interested in killing), then you need to MAKE PEOPLE MOVE away from walls and C'thun's body, because they spawn underneath a player.
I've never seen either of these things happen, btw.
We had also problems with the giant eye tentacels beaming right after they emerged. After 2 days of wiping we simply focussed on naxxramas and didn't bother on C'Thun anymore (have killed him twice before the patch).