This can happen if you rush the Azerite robots and kill them & the missile boats before building at least one Glaive Thrower. The win-state won’t resolve and you won’t be able to engage the end boss since there are no boats for the Glaive Throwers to target.
It just happened to me, because some troll in the instance told everyone to rush without building the siege engines, and we did. We all had to leave, but other people kept joining the doomed instance fresh, and that’s probably what you saw.