^Yeah, I noticed and wondered about that too. Probably a bit of an oversight as you'd think a promotion to full Commander would be a given after the end of ME1 and even that's assuming it didn't already happen when she was given command of the Normandy in place of Anderson.
...but then again by the end of ME3, Shepard will probably be doing the job of a General or Admiral and yet, still a Commander by rank.
Personally, I'm still confused by how Ash who was a non-com in ME1 & 2 is now suddenly a LtCmdr. What was the time span supposed to be between ME2 & 3? Six months? A year at the outside? That's a hell of a promotion. Actually, now that I think about it, doesn't Kaiden (for those who didn't nuke him of course) now outrank Shepard? I wonder how that will be addressed.