You're right that her not being present had a good explanation, which I'd forgotten. However, I don't think that her smirk was a slip-up of graphics. I rewatched that cutscene to be sure that I didn't see it incorrectly. Tataru walks away from you and, after you walk away, she stops, turns, seems to frown, and then smirks. And she isn't the only NPC who does this. During this point in the game, stopping and smirking at the Warrior of Light as s/he walks away is the player's indication that said person is about to screw them over. Her wording was also terribly foreboding.
I might also add that the chimerical gear that she gets for Y'shtola is, according to the NPC that gave it to you, "impossible to come buy unless you have big balls or deep pockets, and that friend of yours didn't look like she had either". Were it just to upgrade Y'shtola for aesthetic purposes, I wouldn't really pay attention to it. But having another NPC point out the impossibility of it sends off a red flag for me, especially considering that the area that you would have to farm chimerical hides from, if I'm not mistaken, is Azys Lla, far before you can reach it. How, exactly, did Tataru come by said gear without our help?
I also find it strange that Tataru is the only character that retains the blind optimism and jolly behavior that characters ARR in HW's much darker atmosphere. This would make since if it were someone that had stood out more, such as Yda, but we rarely ever really dealt with Tataru. Yet a good amount of attention is placed on her ARR-style blind optimism, such as her constant singing and dancing (and even changing emotes depending on when you see her) in the Forgotten Knight. The only time FFXIV pushes background characters to the foreground is when their character is about to change or play a major role in the story, similar to how Yda's mask was given focus in a quest shortly before it cracked in half.
Sorry that I'm arguing nuances and semantics here, but her characterization really seems suspicious when held against circumstance and what other NPCs have said about her.