Corrected entry: The first few projectiles fired on the destroyers by the aliens are taken out by a phalanx CIWS. However these systems use radar to track their targets, and the aliens have jammed all radar, so it shouldn't be working.
lionhead
28th Apr 2012
Correction: When the CWIS BLOCK B1b Upgrade was implemented beginning in early 2000-2002 [and continues to present], the CWIS system gained new tracking / engagement abilities. These include use of a FLIR [forward looking infrared] , AAVT [Automatic Acquisition Video Tracker], and E.O. [electro-optical] tracking. Although not originally intended for engagement of the inbounds found in the movie, it would be possible for an attentive Fire Controlman to successfully engage and neutralize said targets. Reference: http://www.fas.org/man/dod-101/sys/ship/weaps/mk-15.htm.