In Mass Effect 2 it was said that the Geth do not use artificial gravity, yet the Geth dreadnought has artificial gravity.
Upon entering the Geth server facility, Shepard ejects a thermal clip, which is smoking as if the weapon has recently been fired.
During the cutscene just before the run to the conduit beam, Shepard already has his/her weapon out. Just before he/she jumps down, they pull their weapon out again.
Rounds from weapons hit before the visible bolt hits.
Despite the fact that thermal clips are supposed to be universal, one weapon's supply cannot be used with another weapon.
It is not explained where the Normandy crew got a seeker to study.
A Collector has a biotic damage upgrade despite most Collectors not using biotics.
The GARDIAN anti-ship gun's on the colony attacked by a Collector ship fire bolts instead of beams, even though the GARDIAN system is supposed to consist of lasers which travel at the speed of light.
The Normandy's windows do not match the view from outside.
At the last part of the Leviatan DLC, where Sheppard and his team are crash-landing on a derelict ship in the sea-world it's stated that many of them look very old. Yet there are lots of thermal clips scattered everywhere, despite the fact that thermal clips were introduced only 2 years prior the events of Mass Effect 3 game.
During the introductory sequence on Earth, Shepard's mouth doesn't move when he/she says "Thanks, Anderson." this glitch was later fixed with a patch.
Commander Shepard's scars glow, indicating the exo-skeleton beneath.
It's stated in Mass Effect 1, as a major story of the Mass Effect 1 game, that the Citadel is a giant mass relay used by the Reapers as an entry point to the galaxy and that the Keepers of the Citadel are altered by the Protheans so they ignore the Reapers control signals, making their return impossible. However by the end of Mass Effect 3 the player learns that the Catalyst, who controls the Reapers and also the Keepers (who at this point in game are serving the Catalyst in processing the human bodies) is housed on the Citadel itself. That revelation makes the existence of Mass Effect 1 plot useless.
Human lettering and equipment is being used by non-human forces.
The schedule at the Ardat-Yakshi monastery uses human time measurements.
At the very first visit to the Citadel prior to speaking with the Council, player can overhear some Volus diplomat speaking to a Turian diplomat about assisting with "an Alliance project", which at this point isn't even known to anybody but Sheppard, his/her team and Admiral Hackett.
The GARDIAN system on the colony attacked by the Collector ship is a single battery (multiple guns) but is referred to as 'batteries'.
Lieutenant Vega said that Commander Shepard took down the Collector homeworld. Commander Shepard destroyed the Collector Base, not the homeworld.
Cerberus troops occasionally say 'We've got wounded!' when one of their own gets killed even if the character clearly dies.
Ambassador Din Korlack says in a recording that he left a tracking receiver in the office beside an embassy. The Player has to be in the office to access that recording, so the Ambassador should have said '...in this office'.