Suicide Squad: 10 Biggest Questions Left Unanswered
5. How Did Waller Find Out Batman's Identity?
The Question: The mid-credits scene makes it clear beyond all doubt that Amanda Waller is aware of Bruce Wayne's alter ego, when she tells him "You look tired. You should stop working nights." How, exactly, did she figure this out?
The Likely Answer: For one, she's a high-up government agent, so if Lex Luthor can figure it out, it's fairly plausible that she might also with all her world resources.
Going by her meeting with Bruce at the end of the movie, it's possible the two have a tacit working relationship, and don't be surprised if she turns up in Batman's solo movie, either in flashback form or in the present.