I insert an NPC prefab in a scene and i rotate it to 270,0,0 (using the editor). There aren’t any scripts attached to this prefab yet and when i press play to test how it looks like the NPC is rotated to 0,0,0. Any idea about why it happens?
Edit
The npc’s model is animated using mecanim 
Then it is most likely the animation. Try removing the start animation, see if it works, if so then the animation is starting at 0,0,0 world rotation.
I often place animated GameObjects inside an empty GameObject. This makes the animation relative to the Empty GO’s position / rotation. You can then set the parent GameObject’s rotation to 270,0,0 and the animation will start from there, instead of 0,0,0.
Good Luck.