It was strange that he would be left his power and speed but not his durability. What could affect things so precisely as to select only part of his enhancements? ...And did he still actually have a bullet lodged in him? "..What do you mean by not normal?"

Surely he means the monster changes, but perhaps not, because the way they were summoned here implied previously having some kind of enhancements.

SOLDIER weren't, of course, the only enhanced people on the planet. It's possible Vincent was from some other branch, or even some other government. Deepground was a possibility, Wutai was unlikely but not impossible..