Why did the Engineers leave a map to their military facility on Earth?
I have a couple of ideas. At the time that the Engineers left all of those maps, that was their "diplomatic outpost" with sentient life forms around the galaxy. But as we all know, sometimes things change. After a thousand Earth years or so, the planet was repurposed for military testing. "But what about the map hints left on Earth?" They didn't have high hopes for humanity and figured that they'd never make the connection or develop the technology to get there.
I have another idea, that the map was a "trip alarm". Maybe the Engineers had made the determination that if the humans developed in a way that they approved of, there would have been a signal sent from Earth out into space, directed at various places that expected sentient life forms to receive it. What they'd consider the most appropriate form of "first contact." But, if instead the humans made an unannounced visit to the planet outlined in the map, that would mean humanity was inherently hostile. The Engineer being awakened realized "Oh shit, they're here! This went all wrong. Damned it, I've got to kill them all."