When Miguel Alcubierre proposed a "warp drive" solution resolving the prohibition in Einstein’s special relativity on traveling faster than light the problem turns out to be that anybody in the path of the incoming space ship gets fried.
That’s the conclusion of a group of University of Sydney physics students who have re-examined the maths of the Alcubierre drive, and found that when it decelerated below faster-than-light speeds, it would emit gamma rays sufficient to be seriously unhealthy to anybody waiting in the arrivals lounge.
Mathematically, it’s possible to create a bubble of space, with spacetime compressed in front of the bubble and expanded behind it; that bubble will do the traveling on behalf of the spacecraft it encloses, as it were. Inside the bubble, no faster-than-light prohibition is broken. But in the – for want of a better word – "unbubbled" universe, the Alcubierre region can follow a path between two points that allow it to apparently travel between them faster than light.
However, in this paper, Alcubierre overlooked what happens to ordinary matter that the warp-drive spaceship would encounter on its travels.
Hitch-hiking matter becomes planet-killer.
The problem is that the Alcubierre Drive spaceship is going to encounter matter during its trip: space is only nearly empty, not completely empty. Matter traveling towards the ship, the paper says, will become "time locked" with the ship. When the ship decelerates, these hitch-hikers are released from the bubble emitting huge amounts of energy as gamma rays and high-energy particles.
So for answer your question : warp bubble in a planets atmosphere is propably not a good idea...
More detail here (and in this link to the original paper)