Baton Pass is an Eevee level-up move. Egg pokemon only have those moves if both parents know them. So I'm guessing in your case the female Eevee doesn't know Baton Pass.
If you need to have Baton Pass at level 1 for some reason, level up the female and try breeding again, you should get it. Or just level up the baby to lv36 when it learns BP.
Also to be clear, the moves baby Pokemon learn are NOT random. There is a set order like it says on our breeding page - http://pokemondb.net/mechanics/breeding
If the Smeargle knew 4 TMs that Eevee can learn, the baby should have all 4 of them and overwrite any level up moves, etc.
I'm pretty sure every egg you hatch from the same two pokemon will always give you the same moves.