Blue Flower
The rare blue flower that grows on the mountainside en route to The League of Shadows training temple is found by Bruce on his way there. It is a symbol of how some of the most powerful things grow out of the harshest conditions, they must adapt in order to survive and thus they become stronger.
Stealing
Bruce steals products from Wayne Enterprises in Bhutan; it's the reason he is in prison. This is a symbol that he believes his own company is doing things that he doesn't believe in so he goes against them.
Well
A young Bruce falls into a well and is seen being helped up by his father. This memory replays in Bruce's mind throughout his life. It is a symbol of a defining moment in the man's life which causes him to get up over and over again. It is a moment of weakness that become an empowering strength for him.
Joker
We see a joker card in an evidence bag at the end of the film. Gordon is showing it to Batman as he tells him it is a call sign for a new criminal in town. It is a symbol for non other than Batman's arch-nemesis The Joker and means that a new foe awaits the caped crusader.
Bat Signal
The Bat-Signal is used by Lieutenant Gordon in order to call for Batman. It is a symbol that the police work with Batman to stop crime as well as a sign to criminals that the Batman is out for them.