The first line recorded by Bobby in the tea house differs from the first line he heard on his recordings after the whole drama. A dialogue that was not recorded was heard later in that recording.
When Bobby is talking to his chief over phone, to his back, Changez & Sameer are talking to a third person. In the next shot, they are chatting face-to-face.
The envelope pinned on the notice board has different writing (neater, in a straight line, no overwrites) to that on the envelope carried by the girl. It also is missing the creases evident as the girl carries it.
The military men aren't wearing Pakistan's military or militia uniform but Indian Border Security Force's (BSF)
When the photo of the murdered Anse is found, his throat was cut. However, there were only a half dozen trickles of blood. Someone killed that way would have had their clothes soaked in blood.
In Chang's flashback to 2001, Erica takes a photo with her Canon EOS 5D, but the camera was not announced by Canon until 2005.
When Jim & Changez go to Istanbul in 2002, the latter is seen using Microsoft Windows Office 2007 edition, which was released only in late 2006.
(at around 6 mins) The little girl with the envelope marked "U.S. Embassy" is walking through a corridor to drop the brown envelope. As she goes down the stairs, there is a signboard in blue, with white "Hindi" text. This corridor supposedly depicts Lahore and the Lahore Press Club where the signboards would have English and Urdu texts.
At one point, Changez talks about working on the 54th floor of his office building. Later, he says it's the 53rd floor.