I finished my rewatch, and I think I noticed a few things that will come to play later.
Alfred knows who kills the Waynes. In episode 6 he was keeping a secret from The Gentleman Ghost. At first the implication is it is Bruce is Batman, but then it is highly implied it is something Batman does not know. I then thought of what is something so important Bats does not know. I think he found out and keeps it from Bats.
Harley Quinn created the Joker. It just seems to fitting that her plan will go wrong like that. I specifically think it is this guy, as he is the one who actually beat Batman.
Realizing he is the fall guy Harvey Bullock will turn on Flass. In episodes 4 and 10 (same writer) they have a theme that Flass makes Bullock do all the dirty work. Granted episode 3 contradicted this, but that has a different writer. After Bullock did all the dirty work in 4 and is set up to do it again in 10 Harvey Dent reveals this. Later Bullock angrily points out to Flass that is true.
The Animation Historian 