Album covers getting mixed up on phone from iTunes
I had the same problem. Twice... You will most probably have to remove and then re-sync your music.

Attach your iPhone and go to the music section. Remove the check mark to sync music. Your selections will stay intact for later re-sync. Sync your phone. When finished all music should be gone from the phone. Now re-check the mark for syncing music and do the sync.

This fixed the messed up covers for me.