Who says their fuel would have to be combustible? 
Ye, that's also important...
It just seems so unlikely that the alien ship would be so poorly constructed where one area blows up, the WHOLE THING blows up..
This is simply an observation based on its size..
Think about it another way, To travel through space, you would need warp engines that either matches or exceeds the speed of light.. Because if you didn't, why bother going anywhere, just stay home and grow food....
It's like if your only mode of transport is on the back of turtles, foggettabouit.
---- This is a valid comparison given the vast distances in space between any objects.
---- Sublight engine is a no go..
So, This giant ship, has to be rigid enough to be accelerated and decelerated at those speeds.. The construction material must be an order of magnitude more inert than matter-composites..
It has to be something like neutron star matter..
You can blow nukes at it all day, a nanometer coating of that stuff can withstand any current human weapon including nukes..
So, if the aliens has this material, they would surely build core-containment with it.... (the core being likely a miniature black hole)..
And... if we breached containment around even a miniature black hole so close to earth.. Good bye solar system..