Sounds like a bug. Can you assign your Lieutenant Engineer there?
By the way: rank doesn't matter. You can assign a commander BOFF in an Ensign slot or vice versa. In the latter case, you'll only have 1 ability instead of 4, but the game will let you do it nonetheless.
In light of that, you should rank your officers up as soon as you spent enoughpoints on them, it'll make Ground easier.