After the break-in at the Detroit Police Station, a newspaper article refers to Ryan Penn as Chief of Police. He is not, he is merely a police captain.
An email in the Picus Station in Montreal is supposedly written by Nicolette DuClare. This cannot be however, as Nicolette had not been born according to the Deus Ex Timeline. This was most likely meant to be her mother Beth.
A room in the Singapore hangar has no door, only a vent to crawl through.
In a warehouse in China, there are palletized loads on upper terraces but no way that they could have gotten there by forklift because the railing is blocking access to the floor below.
The positions of the Renaissance Center and One Detroit Center in skyline would place the Detroit hub across Woodward Avenue some distance north of the aforementioned buildings, but the avenue is nowhere to be found nor a remnant of it. In addition, the streets throughout the hub, are named after actual streets that are not all adjacent at a block in real life. The game's Milwaukee Junction appears somewhere west of downtown when it should be directly north.
No one seems to mind if Mr. Jensen snoops around in their apartments or offices and takes whatever he wants.
The Player is tasked with deactivating a signal jammer. Since he doesn't actually destroy it, there is nothing to prevent the Opposition from reactivating it.
In certain areas, a passcode may be the same for the whole area, including a passcode to an area beyond a door secured with the same passcode. It would make much more sense to secure all areas with different passcodes.
It does not make practical sense for some items to be where they are, such as finding money at the bottom of a ventilation shaft.
Although Mr. Jensen turned off the jammers in Singapore, there is nothing to prevent them from being turned on again.
The man in the L.I.M.B. clinic in China tells Mr. Jensen to go down some stairs to meet him, but there are no stairs.
In-game text incorrectly spells 'British Columbia' as 'British Colombia'.