I've sorta had that problem. My first play through I used Ashley and Liara as well, I got the achievement for using Ash but not for Liara.
I've read on other boards if you want that achievement with Liara, you pretty much
have to do only the storyline quests till you can get her into your party. That means no extra citadel quests before you're free to roam the galaxy.
As a sidenote, I still haven't gotten the achievement for using our favorite Asari yet.
