The CIWS/20mm Phalanx is the very last ditch defense for incoming an anti ship missile, the Burke class ships have SM2/3/6/etc class missiles for longer range air defense against both aircraft and missiles, ESSM evolved Sea Sparrows for closer in air defense which are fantastic now compared to the older Sea Sparrow missiles. Some of the Burke class destroyers have the new SeaRam rolling airframe missile launcher systems too, not sure if the Mason does or not. And, as others have said, a few ships have laser defense systems, but these aren't optimal for fast missiles and are more for drones, small boats, and slower moving targets - for now. I've read that in the 2 VLS fore/aft launchers for most Burkes, that 72 cells are often loaded for anti air warfare, split by 48 SM2 missiles, 8 SM6/other long range/special SM variants, and then 16 tubes for ESSM which are quad packed, giving 64 ESSM shots. That's quite a lot of firepower for one ship just for anti air ops, not counting the Tomahawks, Harpoons, and anti sub/torpedo missiles either.
ECM is as said a likely defense as well, there are some pretty advanced decoy/chaff systems on board USN destroyers, cruisers, and other warships as well. So, quite a lot of potential ways the missiles could have been defeated, just glad they were. Considering these missiles were pretty successful in striking the recent HSV2 ship, obviously they were stopped by some form of USN defenses, be it passive ECM/decoys or an actual missile/Ciws deal.
