The Marker is at odds with the Necromorphs because while it does create them, it doesn't really control them. The Red Marker doesn't want to start a Convergence event, because it will never complete, Humanity will discover what Convergence actually is and that would be a big unknown to how they would react, also if a Convergence event did trigger then there would be no one left alive to implant the blueprints to create new Markers. The Red Markers 'goal' in DS1 was to find someone to implant the blueprints inside of and get them to leave 'safety' to produce Markers which can have a Convergence event. So that Marker can never be used for a Convergence event. Since the Red Marker was created years prior the 'makers' are long dead and are unusable for convergence. the Red Marker requires the people who made them to be used to complete Convergence. I thought it was because the Markers that are manufactured i.e. So why do they not work together? The remake's version of the Nicole video has her mention that she somehow 'spoke' back to the Marker asking it to stop, but when has a human ever been able to influence a Marker's behavior? It's been a mystery since DS1 first released and I know that it's an oddity that is basically ignored come DS2 and 3 but if anyone has a firm answer to the question in some form of obscure lore or a dev interview I'd appreciate it. We know that the Hive Mind does not want Isaac to return the Marker to the planet, it resists him and sends Necromorphs to stop him every step of the way despite this seemingly being the opposite of what the Marker wants. But DS1 has an interesting wrinkle, in the 'Dead Space' phenomenon and the fact that the Hive Mind seems to be operating at odds with the will of the Red Marker (as portrayed by 'Nicole'.) The Dead Space phenomenon being the fact that Necromorphs can't really get too close to a Marker, and presumably what was keeping the Necromorphs and Hive Mind under control on Aegis VII before it was removed.

Markers drive people crazy and modify genetic code in order to create necromorphs and more Markers. So the Necromorph/Marker life cycle is pretty well described and documented throughout the games.

Dead space 1 necromorph at the end