What Does The Ending Of Suicide Squad Really Mean?
4. Waller Knows Wayne's Secret

Waller trades her exoneration with Wayne for a portfolio on meta-humans including The Flash and Aquaman - which is presumably where he gets his information on their whereabout from. Interestingly, she also hands over information on Enchantress, which could suggest she's still considered a meta- as previously discussed and that Batman is considering her for his team. Let's hope not.
In an incredibly shocking revelation, it turns out that Waller also knows that Bruce Wayne is Batman. As he's leaving she says he looks tired and offers him loaded advice that he should "stop working nights". It's something of a threat, it seems, since you can imagine Waller wouldn't have much time for an unregulated hero operating outside of her control.
And while it sort of compromises Batman's mythology, it does make Waller seem even more like the all-powerful, arrogant machiavellian figure.