Danny's white shirt when they get to the ER is covered in blood. In the following scenes, there is noticeably less blood on it.
When Danny and Linda are at home and she is folding clothes, she turns the same shirt right-side out twice and handles the multi-colored one twice also.
It is standard procedure after any police involved shooting that the officer involved is placed on administrative leave with pay. This is to give time for the department of law enforcement time to examine the shooting, and give the officer time to recover and get counseling from a police counselor.
When the plainclothes officer is running down the stairs, you can see he has the firearm in his left hand, and you can clearly see there is nothing in his right hand. After being shot he rolls down the steps and loses his weapon and you can see both hands are empty. As he hits the ground and is face down, you can still tell there is nothing in either hand, but as Danny rolls him over you see his badge and wallet, which is much larger than his hand.
When Jackie is out on investigations, she uses the witness' landline to call Danny at the precinct. Danny who wouldn't have that number saved in his contacts nor recognize the number and wouldn't know it's Jackie calling, yet when he picks up he answers: "Hey!", rather than the standard "Hello" or "Det. Reagan", indicating that he is familiar to the caller.