I've run through it 3 times and I keep having problems destroying the comet. On two occasions the fragments did not spawn shards when destroyed. On one occasion when the comet was destroyed it failed to spawn fragments. Scanning revealed no interactive objects in the system.
I experienced this as well today. Tried it twice and had to drop both times as no fragments were produced. The second time I restricted my attacks to the comet only, and even let the lead Klingon chase me around for 10 minutes while I went hunting for the non-existent fragments.
I've tried it four times. First time the asteroid just disappeared leaving me stuck, after spending a good five minutes looking for those three fragments. All the other times everything would split except for one fragment that just faded away leaving me stuck with 1/1 destroyed asteroid, 3/3 destroyed fragments, and 6/9 shards.
I've had the problem as well. What I noticed was it happened when I was close to the comet (within a few KM of it) but when I was further away it spawned correctly. So wonder if there's a collision or some other issue being triggered.