The ground explosions were caused by Kalibr cruise missiles targeting the airport terminal nearby to where it appears (from satellite imagery) that the Patriots were stationed. It's perfectly possible that A) all Kinzhal's were indeed intercepted and B) the Patriot battery was indirectly damaged by a nearby explosion but was not even necessarily the target of the missile in question.

It can be very difficult for radars to track objects coming in from a high angle of attack and low angle of attack simultaneously, so IMO the failure to intercept makes more sense from that perspective as well.