As you play through the story you will at some point encounter that you have three missions to choose between, all very close together in a square. The issue here is that once you've chosen and beat one of these missions, the other two disappears, thus you can't get all the achievements in one playthrough unless you save and reload your game.
Before starting any of them, save your game in three different slots to avoid the auto save ruining it for you.
This is three different sub boss fights, each giving you an achievement.
When you have beaten the first one, load another save and go for the next fight. When you've beat the third, continue your playthrough.