In the poem "I Am Goya" by Andrei Voznesensky, what is the contradiction in line 3 about and what does this contradiction suggest about war?

I don't think there is an obvious "contradiction" in line three, unless you mean that the word "gape," in reference to eyes, would usually refer to a form of wide-eyed staring which would take in everything, whereas in this instance, it is the "craters" of eyes that gape. These craters, then, seem to represent only holes where eyes once were, and they gape in emptiness rather than in the attempt to see everything that is going on around them.
This powerful poem depicts the emptiness of war through the use of imagery such as that of the enemy, like a bird, whose "beak gouged" at Goya. War is a contradiction in and of itself: the "craters of [the speaker's] eyes" gape in the sense that the war is too terrible to be understood, and yet at the same time, its destructive power is so great that it has strongly limited what he can actually see.