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.
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
Factual error: 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.
Plot hole: In the episode "Right Next Door," Mac was showing the air duct and saying that the fire would have traveled down the vent to the vacant apartment. The vent was shiny and new looking when it should have been filled with black soot with the amount of fire that traveled down it.
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.
Continuity mistake: Episode 19 - Personal Foul; Lindsay is going through the cheerleaders' photos to find a biometric match of the heavier woman, and she picks a head shot of a blond cheerleader. She removes it from the pile to scan it, seeing through the back, we can see what the actual picture looks like. It is a close up picture of a woman wearing big sunglasses. When the scan is complete, it is revealed as the original cheerleader photo.
Factual error: The plot is about a mosquito who stung the murderer. Although Gary Sinise mentions (correctly) that only female mosquitoes bite, the one caught alive on the table is a male mosquito (look at its antennae). All other mosquitoes used in the episode are female.
Factual error: When Mac is using the mouse to demonstrate induced hibernation to Peyton, the speed of the mouse's heartbeat on the heart monitor was about that of a human. Due to their small size, real mice have an average heartbeat of 500-600 bpm, which is so fast it can sound like humming.
Factual error: During the autopsy of the head, the shot changes to inside the eye, showing the needle entering to extract the vitreous fluid. The inside of the eyeball is shown as white. This is incorrect: the inner lining of the eye is black (hence why the pupil, a hole in the iris, looks black).
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.
Other mistake: Episode 5-19, "Communication Breakdown": When Mac, Stella, and Danny are trying to determine where the fired bullet entered the train car, none of them are wearing rubber gloves. But even though they're not handling any evidence, they're still processing a crime scene.