Plot hole: How could the police miss finding Cybil in the trunk of Michael Zane's car when it was in an impound lot? They would have definitely searched the car if he was found in violation of a federal offence (for carrying the weapons). Even if they didn't do a search, they would certainly have heard the sounds that Cybil would have made from being locked in the trunk.
Plot hole: Murphy and Michael are in jail together, Murphy calls Jack to get him bailed out and tells him that he is using a fake name and he needs to make bail before his prints come back. All telephone conversations from jail are monitored, also, when a prisoner is released from a cell to make a phone call he is cuffed and a deputy is standing with him listening in.