Secondary Research

Some inconsistencies, according to www.wookieepedia.com, include:
In the Galactic Civil War campaign, Darth Vader is present during the siege of Mos Eisley, but in the movie he was on the Death Star while that was happening. And also, as stated in Star Wars novels, Vader would never return to Tatooine for (obvious) emotional reasons.

In the Clone Wars campaign ARC troopers are playable on Geonosis, and Jet Troopers are the new units (instead of ARC troopers) in The Battle of Kamino.

The Trade Federation wins the Battle of Naboo, whereas in The Phantom Menace they lost (although the Trade Federation had the upper hand, until the Droid Control Ship was destroyed).

For an odd reason the sky on Tatooine:Dune Sea is Yellow on the console version of the game but corrected blue on the PC version.

Luke Skywalker flies in a Rebel Snowspeeder in the movie but battles on the ground at the Battle of Hoth in the game.

On the Battle of Hoth in campaign mode, the rebels win instead of the empire.