Anything is possible. This post assumes an Earth-like technology with basically just space-enabled technology. So space-missiles, space-ships, space-mines, etc.
Possible the most effective way to attack an Alcubierre drive ship is to attack it's end point. The Wikipedia article taking about the Alcubierre drive talks about how to travel at very fast speeds using it, you need to begin the process of that travel as many years before as the destination is lightyears away.
Allen Everett and Thomas Roman comment that Krasnikov's finding
"does not mean that Alcubierre bubbles, if it were possible to create
them, could not be used as a means of superluminal travel. It only
means that the actions required to change the metric and create the
bubble must be taken beforehand by some observer whose forward light
cone contains the entire trajectory of the bubble." For example, if
one wanted to travel to Deneb (2,600 light years away) and arrive less
than 2,600 years in the future according to external clocks, it would
be required that someone had already begun work on warping the space
from Earth to Deneb at least 2,600 years ago, in which case "A
spaceship appropriately located with respect to the bubble trajectory
could then choose to enter the bubble, rather like a passenger
catching a passing trolley car, and thus make the superluminal
So if one knew where the ship would end up, one could set-up an attack on the destination.
One could also send a projectile into "the bubble." The missile will then either hit the ship during travel or immediately after it arrives. This would not prevent a ship from arriving, necessarily, but it would likely prevent it from doing anything.
This rest of this post assumes that the "bubble" of space-time created by the Alcubierre-drive does not push all space away from it, so that only the space "native" (i.e. in the bubble when it was created) ever actually enters the bubble. If this is the case, sabotage would be required to attack an Alcubierre-drive ship in-flight.
The most effective way to attack/defend a moving Alcubierre-drive ship would be a mine that attached to the ship. An Alcubierre-drive still requires the ship to pass over all the space it travels through, it just does so at a very fast rate.
Another way is to send a projectile into path of "the bubble" (see quote above) that the ship will be traveling through. It would have to travel along the same route of the ship, but in the opposite direction, because estimation of an Alcubierre ship's position would be difficult to impossible.
Wikipedia says that the above to methods could work, because
A paper by José Natário published in 2002 argues that crew members
could not control, steer or stop the ship because the ship could not
send signals to the front of the bubble.
So even if they knew the mine was in their path while in the bubble, they could do nothing to prevent the inevitable explosion. This might result in the sending out of "dummy ships" to blow up mines and missiles before the main, expensive ship comes.