Plot hole: To identify the owner of a severed leg, Pride asks Loretta if she can guesstimate the body's general build by the foot's boot size. A much simpler way would be to swab for blood where the leg was severed and run it through the military DNA database.
Plot hole: A major plot device is Harry's fingerprints on a whisky glass at the murder scene. We see the glass being taken after he drinks from it at a bar. Why are there only his prints on it and not the bar staffs'? And why does no-one wonder why the victims prints aren't on it as well? If they think it is an attempt to frame him, why do they not even check if it matches any other glasses in the apartment or is an odd one out?