No, that line makes no sense. Of course they knew exactly where to hit them. Its another Starfleet vessel that fired on them, not some unknown vessel.
It makes all the sense it has to. It's simply a character's reaction to the precision with which the other ship fired on them; it's scarcely an expression of surprised astonishment either here or in TWOK.
As directed by Meyer and delivered by Nimoy, it's a great and effective line: terse, efficient but with an edge of alarm at the unexpected in the middle of a tactical disaster. Part of the ratcheting-up of the tension in that scene.