I am assuming they are some kind of weak spot but is there anything behind this. Do they mean something specific as I have often shot an enemy in the leg and the orange marker will just vanish. I cant hit them there again.
This orange marker is a way to instantly deplete an enemys guard. So if you hit the point, the enemy will become stunned and you will be able to perform a stun attack on them which is normally an instant kill. Some enemies will have more than one of these. You will need to hit all points to fully deplete the enemies guard. Shots to this spot will also do damage but its not really a traditional weak spot.