In certain circumstances, Bootcamp can mess up Fusion drive formatting. Here is a detailed posting of how to recover your drive. It basically entails, booting the Internet Recovery from Apple Restart by pressing alt cmd R at startup and then using a series of diskutil commands to first remove, replace and rebuild the logical disk.

It seems that a “fusion” drive is really a “logical” drive made up of two (or I suppose more) physical drives …

See all the ugly details at:
http://apple.stackexchange.com/questions/168723/i-think-i-messed-up-the-fusion-drive-on-my-1tb-imac-with-bootcamp