Plot hole: During the shootout with Penguin and his gang at the warehouse Batman gets shot and falls to the ground. Penguin then creeps over to the spot he fell and realises he has disappeared and is in his car behind him. It is totally impossible for Batman to just disappear and get behind them without being seen, no matter the rain or firefight, that place was lighted enough and everybody was looking that way. (01:18:00 - 01:19:15)
Other mistake: When Batman is video calling the Riddler and passes the phone over to the D/A, you can see Batman's face still looking at the phone in the reflection of the Riddler's glasses.