I plant the first bomb on the ship, and the objectives in the Quest Tracker update accordingly.
I plant the second bomb at the scrying crystals ... and the quest disappears entirely from the Quest Tracker.
I'm not sure if it's planting the bomb specifically at the scrying crystals that makes it vanish, or if it's simply planting a second bomb that does it. I'll try them in a different order next time to see what happens.
In any case, this is an annoying issue. Given that I have seven quests active while doing these dailies, with many objectives, and given that I have to be constantly aware of my surroundings since I'm flagged for PvP and may actually end up in PvP at any time, I count on being able to review my progress to see what I still have left to do. Particularly if I'm interrupted by PvP combat.
So when the quest vanishes from the Quest Tracker, it's very easy to forget that I still have one more bomb to plant. So I get everything else done, my Quest Tracker is showing all my objectives completed, and I teleport back to Violet Rise ... only to realize I forgot to plant that last bomb.