After their wedding, when they're leaving, Scott has his shades on when he opens Jean's car door, then they're not there, then they're on again.
The leader of the group that goes after Apocalypse states that the world has had to put up with Apocalypse's evil for 5,000 years. Seconds later he states that Apocalypse has been wreaking havoc for "500 centuries" which would actually be 50,000 years.
Dated 3999AD, Cable states that Apocalypse has been terrorizing for 5000 years dating him at 1000BC. This is not possible because Apocalypse come from Ancient Egypt set in 3000BC.