When Johnny Cage takes a blow to the crotch by D'Vorah in the first fight, Sonya tells him, "Don't be such a baby; It's just a kick in the nuts." However, the animation shows that it was actually a punch to the nuts, not a kick.
Li Mei (who Sonya fought in her first tournament match) is labeled as "Mileena" in the end credits.
Raiden loses his godhood to fight in the tournament, but Shao Kahn (who mostly likely is a god being older than 10,000 years and can who can consume souls) gets to fight in it without losing his.
In her fight with Shao Khan, Sonya Blade is stabbed in the leg with a spear. Moments later she walks correctly throughout the rest of the movie without limping.