After the bookie's safe was cut open with a torch, none of the money inside is damaged. Torching open a safe will damage or destroy anything inside that is even remotely flammable.
The inside view shown when the officer removes the safe door shows the locking bolts retracted, meaning the safe wasn't locked.
Pepper passed when salt was asked to be passed. This occurred just after everyone was "caught" trying to help Danny when they said they did not.
The bookie was shot with Danny's off duty weapon. They never state the weapon was at the scene. So how did they match ballistics? There would no reason for his weapon to to on their ballistic files.