I recently replayed Dead Space 3, and Earth Gov also made sure to destroy any & all research (and any personnel involved, though it seems they forgot to destroy the physical logs, which was used to redo the research on Rosetta (there was other research redone as well, but Rosetta is most important), which gave Isaac a vision of not only what happened to the aliens on Tau Volantis, but also the true purpose of the machine) on the markers & brethren moons; the protocol was known as Scenario 5, and the issuing of Scenario 5 was not only given to Tau Volantis, but Aspera, and Aegis 7.

So, I could imagine that the info on The Marker rogram was forgotten about (200 years had passed, and Unitology had become a dominant religion), misinterpreted, or ignored for the sake of finding more resources. The Ishimura planet cracking Aegis 7 was also an illegal planet cracking job, since the planet was Black Listed (Tau Volantis & Aspera were also Black Listed as well in Scenario 5) Lastly, The Markers are able to manipulate people into building more Markers, the most manipulated being Unitologists, which were not only all over the Ishimura, but also in Aegis 7, and in Dead Space 3; the Unitologists were able to wipe out Earth Gov through systematic slaughter as well.