Unless I'm mistaken the 'scientist' alien knows this all along, and has been searching for the black fluid all this time.
Remember when the ship first arrives and humans explore it they find what they described as two castes, the warrior/worker ones far outnumbering the other smarter kind (or I am mistaken and they feel they are only the soldier caste, and the smarter leaders must have left).
So no one, no one at all is looking for the black goo in the whole of district 9, as the lone scientist is the only one who knows enough to do anything about it.
Further more the scientist alien needs to get up to the ship anyway, and open it up. I remember they need the goo to do that too. So there could have been gallons on the mother ship, but none on the ground.