Shepard can be seen, along with other Team Members, holding and firing the wrong Assault Rifle during the finale cut-scenes.
Enemy shields do not recharge, despite them recharging in the first game.
In conversation, Joker wonders if he should worry that Kasumi pawned parts on the Citadel - even if the Citadel has not been visited between getting Kasumi and speaking with Joker.
The windows on the Normandy are different on the outside.
The researcher's log on Project Base indicates surprise when Shepard's sedatives aren't working, yet later she is surprised when they aren't working.
In Local Cluster, the planets are all seen with retrograde rotation (clockwise as viewed from the north pole). Only Venus should have a retrograde rotation.
Dr. Mordin Solus' cure is sometimes called a vaccine. Vaccines are preventative and do not work on the already infected.
Haestrom is listed as having 0.0 Earth atmospheres of pressure. If this was the case, there would be no air to breathe.
On the CIC, Captain's Quarters, and Engineering decks of the Normandy, the elevator opens towards the bow of the ship. But on the Crew Quarters deck, the elevator opens towards the stern of the ship. The elevator on Normandy SR-1 also opened on both sides, so this is not unreasonable.
In the codex entry of the Mass Relay the still image of the relay has a "LOADING" watermark in the lower left hand corner of the codex's image, even though nothing is loading when reading this entry which means the image is a direct screen shot grab from the first game.
Grammar mistakes in subtitles.
Sometimes enemies say something after they have died.
The inside of Liara's mouth glows blue.
If the Player cloaks, enemy NPCs can be heard saying the line that they would say if this happens in combat, even if the enemy NPCs haven't seen the Player yet.
In the beginning of the game, Joker faces a decompressed interior of the Normandy with only a helmet. A helmet is not enough to protect against the temperature of space.
The handgun that Shepard gets from the locker in the med-bay at the start of the game has no thermal clip (or so Shepard says). Despite this, one is ejected when he finds a thermal clip, this despite the weapon not being fired.
The Mako on the crashed Normandy is too small to be able to fit 3 crew within.
The Zakera Cafe and others don't have any food-service equipment.
Some text on screens is upside-down.
When 'Archangel' tells Shepard that the mercenaries are breaking through the door, his mouth doesn't move.
Some characters have glowing bellybuttons, which indicates that the exo-skeleton (which glows if not covered by skin) is behind.
Shepard's scars glow. Below the surface of digital objects in a game, the objects glow, so this indicates that the scars are simply tears in the digital surface rather than an attempt to make them look real.
The Hugo Gernsback crashed ten years before the events of this game but the crew drop heat sinks when they die. Disposable heat sinks were only integrated in weapons of organics after the geth attacked the Citadel.
Neural hacking can somehow generate a shield around a synthetic target - even if the target isn't equipped with one. It is not explained how this is possible.
Rana Thanoptis has clothing with 'Dr. Chakwas Medical Officer' printed upon it - despite not even being on the Normandy.
It is not explained why 'Archangel' had not closed the downstairs shutters across the bridge at Omega Station.
Although having a low oxygen level and air pressure, Artoht does not require oxygen masks to live on.
Miranda says that she worked on the Lazarus Project for 2 years, yet later when she mentions it, Shepard has the option of being surprised.
At the end of the mission to free David, if David is rescued, Shepard tells Joker to contact 'the Academy', without specifying which academy (Grissom Academy).
The human at Omega trying to get into Aria's is repeatedly told to get in line despite already being in line.
When 'Archangel' and Shepard meet, Shepard says that 'Archangel' nailed him pretty good, even if Shepard didn't get hit on the way in.
Shepard notes that transparent material is a structural weakness on the Normandy, but he only ever mentions this on the starboard observation deck. He never mentions it when he first sees the Normandy.