Plot hole: Why do Dr. Beckett and Dr. Keller use so much Earth medicine? While the Ancients may have evolved past disease and genetic defects, they would still need treatments for physical injuries. And we know such advanced medical machines exist, scanners have been shown on screen and the Go'auld reverse-engineered their sarcophagi from an Ancient device. While they may be reluctant to use unknown machines for surgery or disease, surely bruises and broken bones should be healed instantly!
Deliberate mistake: As the Wraith "stun bomb" activates at the SGC and everyone falls to the ground, it is visible how everyone uses their arms to dampen the fall.
Audio problem: In the scene in the hallway when Sheppard and Teyla are dressed in hazmat suits and talking to Dr Weir via the intercom, you can see a reflection in Teyla's helmet of Sheppard's mouth moving, but there's no sound. (00:23:45)
Character mistake: Rodney says that one hour in real time would give them months inside the field. This is incorrect because if the ratio of time were 1:250 as stated before, one hour would only convert to 250 hours, which is 10 days and 10 hours.
Visible crew/equipment: When Novak is talking with Caldwell on the comms about beaming a nuke inside the ship, you can see an arm in Hermiod's "butt" moving with Hermiod. (00:08:30)
Character mistake: General Landry says that the Asurans would need to rewrite McKay's macro to gate to any planet in the Milky Way. In fact they wouldn't have to bother with the macro, because they could simply gate directly to the Milky Way from a ZPM-powered Atlantis.
Character mistake: It is mentioned the previous solar flare was 15000 years ago, and Shepard says that the ancients were in the middle of a war with the wraiths, but as stated in previous episodes the war lasted 200 years and ended 10000 years ago. (00:31:30 - 00:38:10)
Continuity mistake: Before Merell enters the cage to be fed on by the Wraith, his collar is open. Next shot when he enters the cage the collar is fully buttoned. (00:28:08)
The Eye (2) - S1-E11
Visible crew/equipment: In the beginning of the show (before the intro starts), when you look out the window you can actually see two people shaking the small trees in the storm... Come to think of it, why would there be trees in the first place? How could they survive out there if Atlantis submerged in the ocean? (00:02:21)
Continuity mistake: Lt. Colonel John Sheppard is packing his belongings up and his skateboard is against the wall at first, then it is on top of boxes.
Continuity mistake: At the end of 2-2, Runner, Weir shows Ronon images of the destruction of his home world - a fact he had been unaware of. But in "Trinity," Ronon says "all these years I thought I was the only survivor."
Character mistake: In the first few moments of the episode, as the survey team walks through the halls, the German member of the team is wearing his flag patch upside-down.
Other mistake: McKay and Jackson enters a room and runs into 2 armored figures, Jackson eventually reveals that they are empty suits, however in every shot shot from behind the suits, the suits are constantly moving, as if they are hanging on strings.
Audio problem: Teyla's audio sounds way more high pitched then normal, either dubbed or a post production mistake. (00:06:00)
Other mistake: In Shepard's apartment, there is a fresh pineapple and other fruit in his kitchen. This despite him having been in Atlantis for several months. This later turns out to be an artificial reality, but that should've been a big hint.
Revealing mistake: Steve (Wraith)'s belly appears not to match the rest of the Wraith character's skin tone. Clearly, it is a human body rather than an alien. (00:31:36)
Continuity mistake: During the episode Ronon has flashbacks and keeps referring to "the gate" when trying to make his wife leave. It was only after Ronon met the team from Atlantis he begun using the term Stargate as most (if not all) prople in Pegasus refer to the Stargate as the ring of the ancestors.
Quarantine - S4-E13
Revealing mistake: When Dr. Zelenka drops into the room from the ceiling vent, the wall with the monitor projecting the map of Atlantis vibrates as he hits the floor. (00:38:00)
Continuity mistake: In several scenes (mostly on the planet) we see characters reacting to tactical information from the oracle as if it's displayed in real time. However, the units in the display are moving far more quickly than they could in real-time.
Answer: Those are actually suits that protect from hazardous chemicals. They are cheaper for the prop department and look nearly the same as biohazard suits. A real biohazard suit would indeed have a helmet that seals to the neck.
Grumpy Scot