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.

Continuity: Season 3, Episode 11 (Raising Shane) Just as Casey is caught we see Detective Flack tackle him to the ground. The moment before Danny jumps on top of Casey we see that he is lying on his side. Yet when the camera changes position he is lying on his front.

Factual error: Season 3 Episode 54 (Murder Sings The Blues). Several police and crime lab personnel are in the train car looking at the dead girl and discussing the possibility that this death could be the result of a bio-hazard or chemical hazard. Later in the episode, ebola and anthrax were discussed. These are level 3/4 hazards which require Hazmat suits and oxygen supplies. At the very least, there should have been very serious access control to the scene. None of them are wearing any type of protective gear except rubber gloves, and there is nothing more than standard crime scene access control. Contrast this with a scene later in the same episode where 2 characters in the lab are wearing respirators when dealing with the dust and other stuff from vacuum cleaning system. If the CSI team or the police really suspected that there was a biohazard or dangerous chemical agent present at the crime scene, then their behaviour was quite cavalier under the circumstances.

Factual error: Season 3, episode 49 (Not What It Looks Like). Breaking glass with sound is possible, but would not work as depicted in the episode. First, in order to break the glass, you have to force the glass to vibrate at its natural frequency - that is, the frequency at which it would vibrate if it were tapped. Each piece of glass has its own natural frequency, depending on a range of factors including size, chemical makeup, shape, hardness, and manufacturing methods. No single frequency would shatter all the glass in the store at the same time. Finally, in order to break the glass the piece has to be closed-ended. You can't shatter a plate of glass with sound (nowhere for the sound waves to resonate). Please see http://www.madsci.org/posts/archives/feb98/887203231.Ph.r.html

Audio problem: When Mac and co. enter the basement of the house in Queens (the one where the third woman was found) the record player lifts off its needle and moves to another spot on the record, cutting off the sound for a second. However, the music starts again slightly before the needle hits the record.

Other: While investigating Corporal Price's death, Danny comments that Price was "found dead at midnight." Price was found the following morning; Danny should have said Price died at midnight. For someone who investigates murders for a living, that's not a mistake he would make.

Plot hole: In episode "And Here's To You, Mrs. Azrael": They state that the heart monitor on "Nicole" never showed any movement at all as she was being smothered, because the killer swapped it out and put it on herself. When Mrs. Rollins was smothering her daughter thinking it was Nicole, her heart rate would have raced and her blood pressure would have gone up a little as she strained to hold the bag over her face. The monitor would have picked that up.