Not level where drywall and backer board meet
Once you tile, it wont' be that far off. However, if you aren't planning to use thick tile, you may worry about that edge potentially seeing a lot of water. However, there's a lot of ways to deal with this:


Install a plastic corner bead where the drywall meets the backer board and plaster over it. (I'd probably solve this way)
Install some matching chair-rail or bull nose tile that could hide your mistake.
If your mud isn't set yet, just remove the backer board from the wall and add some strapping behind it.
Finally, you could just add add another layer of backer board.