It's not that, it began in the production of Chrono Cross. They made the mistake there, when they removed Magus from the game due to an overload of characters that weren't connected to the story. Right now they're just trying to correct it by making it look like Magus became Guile at the end of CT.
Actually, I don't see it as a mistake, as I never really liked Magus at all, and I love playing with all of the 40+ characters in CC, loads of variaton. It's just that, most people loved Magus, and are now shocked how Square is trying to link him with Guile.
I can understand that viewpoint, but yeah.