Plot hole: The CSIs catch a murder suspect putting down a drink can when reviewing security footage of a robbery, and immediately realise they didn't see it at the scene so assume one of the first cops on the scene must have removed it. Thing is though, the murderers shot out the security camera before the actual shooting occurred, meaning there was loads of time off-camera for the killers to take the can with them, but the CSIs never even consider this - they jump to the conclusion a cop took it even though there's no actual evidence for that.
Plot hole: In episode "Silent Night": When the mother checks on the baby in the first scene, you see the killer knock over the snow globe. The mother wouldn't have heard it since she was deaf, but she would have felt the vibration on the hardwood floor from the heavy object hitting the floor.
Plot hole: At the end of the episode, Stella and the others determine their rape suspect is guilty because they confirm the tree sap on his clothes transferred to the victim's underwear. That transfer should have been discovered, if not blatantly obvious, during their initial processing of evidence.
Plot hole: In Episode 4-4, "Times Up," it is stated that Kevin Murray will be killed at 9:45. When Mac is standing over the dead body, he looks at his watch. It is 9:45 and he says, "Right on time." Unless Mac was standing on the sidewalk when he flew out of the window, he actually would have died earlier, since it would have taken time for the police to be called and arrive on scene.
Plot hole: The coroner found the ticket stub in the throat of the guy whose tongue was cut out, he died in the ER. The ER staff would have have found the ticket stub while trying to save his life. With the tongue being cut out they would have opened up his mouth to stop the bleeding.
Plot hole: When Sid and Hawks are telling mac that the piece of glass from the girls shoulder is from the window from bar, Sid tells Mac the scar shows it healed in the last month, but it's been established several times earlier in the episode that the bar shooting happened 3 months earlier.
Plot hole: At the end of the episode, Adam and Stella are checking how many others there are bearing the same name in a government database. "Stella Bonasera" gives one result, being the Bonasera character. A search for "Sid Hammerback" also gives one result, a 90 year old woman (the characters say it has to be his mother). But Sid himself should have shown up too, with the search yielding two results, not just one.