Ilia was last-minute, but that doesn't necessarily make her a replacement for someone else. After all, the Enterprise
was rushed into service to intercept the "intruder." It wasn't supposed
to be launched for days, even weeks, and that would've just been for a shakedown, not active service. So they didn't necessarily have the full crew complement already assigned and ready to go. They were scrambling to pull together enough personnel to let them launch in 12 hours. It's not unreasonable that some of the posts weren't filled until late in the game.