If an officer or CSI is involved in a shooting, either as the shooter or as a witness, they are not allowed to be involved in the investigation. But Mac analyzes evidence from the scene, goes to question the suspects mother, and chases down other suspects.
Even though the shooting suspect turns out to be a Confidential Informant, he would not just be set free at the precinct. If he was essential for an ongoing investigation, he would have been covertly put back on the streets without his cover being blown.
After removing the victims thigh bone, Hawkes is shown twisting it to get the bullet to work itself out. But since the femur (thigh bone) is the strongest bone in the human body, Hawkes would have had to use a vice and a pry bar to get enough twist to get the bullet out, not just his hands.
Bonasera finds a .40 caliber shell casing, a closeup of the case's head is shown, it has ".40 CAL" stamped on it. A cartridge case would not have just the caliber stamped on the head, it would have the specific cartridge type stamped on it. There are several .40 caliber pistol cartridges (and many rifle cartridges) and they are not compatible with each other, which is why it is critical to have the exact cartridge stamped. By far the most common pistol cartridge of this caliber is the .40 Smith and Wesson, which is abbreviated on the head stamp as ".40 S&W".
The Medical Examiner Dr. Sheldon Hawkes removes the entire femur from the victim so that he doesn't damage the bullet that is lodged in the bone. That would have meant cutting the entire thigh open, and cutting all of the muscles and ligaments that were attached to it. The faster, easier and more proper method would have been to expose the bone on both sides of the bullets and cut that section of bone out.