On Noveria the Mako is in the garage despite Shepard needing a pass just to get in, and the Mako being in the Normandy's hold if the Player gores to the Normandy.
If the Player romances a character, the Normandy will go through the Mu relay twice.
The timeline in the Codex lists the 100th anniversary of the first moon landing as July 24, 2069. The actual date of the first moon landing was July 20th, 1969, not the 24th.
Upside-down lettering on panels.
Some rapid transit stations are in places where air cars couldn't possibly get to, like in enclosed places.
The ship's head (toilet) on the Normandy is mentioned, but no head can be found anywhere.
There are few chairs aboard the Normandy. Humans need to sit after a time.
The Mako is too small to fit 3 people inside.
Geth spaceships may pass overhead when the Player is exploring a planet, but they do not attack the Player.
The Rachni are labeled as such on the combat display before Shepard and the team even hear about them, and despite this the Rachni still come as a surprise when mentioned by name.
Matriarch Benezia tells Commander Shepard that the Mu relay was propelled out of its system by the nova of that system's star, and it was later obscured by the nebula created by that nova. Given that an object continues to move in space unless it's path is obstructed by something, the Mu relay should have moved past the nebula since it was pushed out of the system before the nebula formed.
The amount of husks aboard the Cornucopia indicate a crew much larger than would be needed for a vessel of that size and function.
On Noveria Shepard and his team do not seal their suits when going into quarantine, as any reasonable person would be expected to do.
Admiral Hackett says that the Geth that the Player is tasked with rooting out must have been preparing for a major offensive in 'the system', even though the mission takes place in a star cluster and not just one system.
Lilihierax calls Synthetic Insights 'Synthetics Insights'.