In the mission haunted cathedral Garrett goes to the back of the Cathedral where there is a hole in the wall which the eye talks to him threw, but when Garrett returns 3 missions later you go behind the cathedral and there is no hole there.
Guards and soldiers are shown with their swords in hand all the time. Swords are too heavy to be carried constantly in the hand and usually are kept in a scabbard on the waist or on the back when not in use.
Some places such as the Thieves' Guild are underground in areas with no ventilation. Especially considering that there are fires and torches in these areas, they should be uninhabitable.
On the level the haunted cathedral you can destroy the three haunts in the cathedral through the hole in the cathedral but when you return there 3 missions later the 3 haunts are back.
The Player is somehow able to steal from right in front of NPCs, which shouldn't be possible.
NPCs do not react to arrows being used nearby.
The intro of the game has a message about if the thief gets caught that " Ye shall be driven forthwith" Ye is plural the line should be thou shall be driven.
A note by Raul describing his theft of provisions and a secret passage in Lady Valerian's home is conveniently left on a table accessible to Lady Valerian's guards.
The items that can be purchased at the store are more expensive than the loot that can be obtained on a mission, which would make each mission ultimately not worth it.