The blast damage and blackening seems to me to indicate the missile came in at enough of an angle from the starboard side to allow the Phalanx to engage. I could easily be wrong and will have to wait for more data.
I'm looking at the dispersion pattern on that picture. It looks like it came from astern, and at a slight deflection such that the superstructure would block the Phalanx guns.
Also, remember that Phalanx has to be pointing in the general direction of the threat to start with, on these ships - they don't have Aegis to cue the Phalanx system's radars, plus they have the "man-in-the-loop" version where a human has to okay the attack.