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: Danny explains how the glass was broken using ultrasound waves to hit the glass at their resonant frequency. He explains it could be done using a mp3-file and a mp3-player. As mp3-players are designed for the human ear, the upper frequency limit is around 20 khz, far too low to produce a sound capable of shattering glass.
Revealing mistake: After Danny breaks the glass in the lab allegedly using sound waves, you can see in the shot immediately after the glass breaks, a thin green laser beam from roughly further top left to near bottom right. It's assumed this is what actually broke the glass.
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).
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.
Factual error: 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: 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.
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.
Audio problem: During the sequence where Lindsay is telling them about the tape with the lipstick on it, they show a man tying up a woman. You hear the sounds a woman would make if she was muffled by a gag (tape) on her mouth as she's being tied/struggling throughout the scene, but her mouth doesn't get taped until the end of the scene.
Character mistake: As Peyton is examining the body and reporting her findings to Danny at the beginning of the episode, Mac picks up a credit card he deducts was used to open the door, but he isn't wearing gloves; this would compromise the evidence even if by holding it by the edges he preserved the prints.
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.