Had the same bug, had to replay this 4 times before it triggered. Has to do how the plague carriers spawn in the last area, make sure to lure them before the tower explodes at all costs even if you wipe or else it will bug out.
ArenaNet please look into this ASAP, I used up 1 hour just to complete this and was increasing frustrated every time — the spawning of enemies within the towers NEEDS to be fixed since I also saw enemies spawn inside the rock AFTER the explosion and they were stuck and could of added to the game breaking bug. Luckily I had AoE spells to take them out!