Yeah, I was left wondering that too.
She casually murders whoever gets in her way, but she goes out of her way to avoid killing her former classmates. She spares Armin and she lets the big blonde guy (Rhiner? Reiner? Rhineheart?) get away even after grabbing him out of the air. (Is there something going on between those two? She takes a lot of her cues from him early on and they're often seen together.)
She also doesn't kill Eren despite having multiple chances to do so. Once when she was carrying him in her mouth and once during the final punch-up when she smashes his titan's head into a building, knocking him senseless, then just runs away instead of chomping him.
So she was presumably acting with the intent to kidnap Eren, but not harm him.
There's apparently some kind of faction of titan-shifters who are intent on fucking up the human cities. However, Annie expresses remorse at the deaths incurred during the battle in Trost. So they're letting the titans in, but feel bad about killing people in the process? But are implied to have delayed the breaching of Trost upon discovering Eren's abilities and are willing to kill people like flies in order to capture him?
I guess they were trying to recruit Eren then? Titan-shifters are presumably pretty rare.
Eh, whatever. I just hope she comes back and explains herself at some point. I kinda liked her character. Quiet and driven and gets shit done. Although I'm inclined to like anyone who beats the shit out of Eren.