Despite being larger than Tyrannosaurus, Giganotosaurus is not nearly as large as the character in the game is. In addition, the Giganotosaurus in this game bares only 2 fingers when in reality they had 3. The Giganotosaurus is obviously a scaled-up Tyrannosaurus with everything unchanged.
Container blocking the military facility's entrance (where Dylan's first encounter with T-Rex) disappears completely in Regina's scenario and onward.
In the prologue, it is mentioned that only one year has passed since the incident occurred in the first game. However, when Dylan retrieves memo from medical room it is reported that 10 years has passed since the "overdrive" incident transports them into another time. Whether it is time dilation, or fictional physics errors, is never mentioned throughout the game.