This is a "port"; a remake of the original game "RockMan X", made in 1993 on the Super Famicom (SNES). Some of the aspects of the game have changed, including plot, character backgrounds, and future installments from the time of creation.
Vava (Vile) was originally an Irregular Hunter (Maverick Hunter) apart of X's 17th Unit. His reason for turning Irregular in the original was simply because Sigma promised him power, and the chance to destroy X. In this game, he is a rogue who does not obey anyone.
In the special anime sequence, The Day Of Sigma, it shows Sigma receiving his eye scars by X. However, contrary to this, it is shown that his scars are from his first encounter from Zero from the RockMan X4 anime.
In the special anime sequence, The Day Of Sigma, it shows the death of Dr. Cain. However this is also controversial to RockMan X3, in where Dr. Cain is alive and aides X and Zero.