are mines considered obstacles? just wondering if i could avoid the effects of Mines using Chart Officer, says "if you overlapped an obstacle" you and discard chart officer to avoid the effects of the obstacle.

They are not. The types of obstacles are listed on RRG 8 - OBSTACLES, and they're just Asteroid Field, Debris Field and Station. Because of this and the fact that the objective card doesn't specify that they are obstacles, there is no reason to think that they would be.

Your Chart Officer may know his space maps, but he doesn't know where your enemies laid their space mines last night before you hyperspaced into battle.