The Alcubierre drive is a special type of theoretical FTL engine. The physics stack has a tag for Alcubierre drive and 161 questions! https://physics.stackexchange.com/search?q=alcubierre
A drive comes with specific dangerous downsides: 2 I can think of. To work the A drive requires a specific form of exotic matter: negative mass. Negative mass exists on solid theoretical grounds and so tweaking its properties is probably disallowed.
That hole in front of the ship is supposed to be where space is crushed very small. The red hump is where space is created.
Here is a non-danger of the A drive: whacking into stuff with a huge amount of kinetic energy. It achieves FTL travel because the ship does not actually move, but instead it moves space around it. It does not have any kinetic energy because it is not moving. That is how it does not violate the rule about FTL. Space is crushed to a singularity ahead of the drive and in effect "created" behind the ship. Once the drive is turned off, as I understand it the ship is sitting there. This is unlike some rock which comes hurtling in at the speed of light or more or less and whacks into something with tremendous kinetic energy.
Here are 2 dangers.
1: Warping space (crushing it to a point) warps matter in it. That is bad for the matter (like a planet or a ship) because it is crushed into a singularity ahead of the ship. So your ship would destroy whatever it drove through. But some people think the nature of the drive means it would not interact at all with matter outside the field.
This 2-dimensional representation of spacetime shows that it would
exclude interaction with any baryonic matter between outside and
inside of the ripple while such drive would be able to warp spacetime
around it, but at the same time does not prohibit normal interaction
with matter inside it. This means that, unless you've created a ripple
large enough to include in it an object already on collision course
with your spaceship before you turned your Alcubierre drive on, or
turned your drive off at an inconvenient place, you wouldn't have to
fear collision. Well, that's to my understanding at least, it's not an
easy idea to wrap one's head around.
- Turning off the drive releases the negative matter singularity ahead of it, and any matter accumulated in the crushed space there explodes with huge amounts of hard radiation.
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.
But if this drive fails to interact with any matter in its path as posited by Tildalwave above, this would not be a problem either: the singularity would warp only the empty space in the vicinity when it started.
If you make your Alcubierre drive fail to interact with any normal matter when it is on, it cannot be weaponized. A moving ship in the warp moves through whatever it encounters. When the ship stops and turns off the compressed singularity in front of it, nothing happens. This drive could be used to warp a sack of dog poo (or a bomb) inside another ship and then materialize inside it by turning off the drive, but this is not a threat on the order of light-speed impactors.
Here are two reasons to make it unlikely there will be warp bombs.
1: When bomb goes off you lose your A drive and the exotic matter. This is a lot more expensive than rocket fuel.
2: It is hard to steer. When you are in the A drive you cannot see outside the bubble. If you have the "speed" of the object inside the drive vary according to unpredictable factors one could have these ships emerge from the warp bubble within a fairly large possible area. Cargo and personnel ships will want to emerge in large empty spaces (possibly cleared in advance of their arrival) to minimize the chance of appearing in a solid object. Your A-drive warp bomb might emerge from warp several thousand km away from its target.