The Belgrade level's loading screen says that it takes place in February 1999, but the data sticks you encounter in-game give the date as April 1999.
Sam is shown working for Third Echelon in 1999, however the first game of the Splinter Cell series says that Third Echelon was not founded until 2003.
Sam is shown working with Grimsdottir in 1999. However, in the first Splinter Cell series game, he meets her for the first time in 2004.
In the Penthouse level, the ARNG soldiers are using QBZ-95 rifles. The U.S. does not use this weapon, since it's a Chinese one.
NATO is shown bombing Yugoslavia in mid-February 1999. However, the bombing campaign did not start until late in the following month, in March 1999.