The Hand Behind The Scene.

The surveillance and sensory systems of the Leviathans can't tell who or what he is. If not for the warping of space, which they are extra sensitive to, then they wouldn't even know that someone was there. 

It is as if there is a blind spot in their senses. If not for the fact that they are nonliving and have no consciousness or cognition, they would have instinctively ignored the perception of the warping space around them.

Unfortunately, they are cold machines, so the little discrepancies in their sensory data didn't escape their notice. Instead, the anomaly made the Leviathans prioritize eliminating him. 

But it is easier said than done. They can't track his movements fast enough, so their attacks are always one step behind. They made up for that with the generous use of carpet bombing. But even then, they always missed him.