This may explain why we have not shot down the past two launch is over Japan. The headline is a little misleading. It's not that we can't at all, we just can't fire at the missile when its apogee is beyond the defense system.
No, We Cannot Shoot Down North Korea’s MissilesThe number one reason we don’t shoot down North Korea’s missiles is that we cannot.
Officials like to reassure their publics about our defense to these missiles. Japanese Chief Cabinet Secretary Yoshihide Suga told his nation after last week’s test, “We didn’t intercept it because no damage to Japanese territory was expected.”
That is half true. The missile did not pose a serious threat. It flew over the Japanese island of Hokkaido, landing 3700 km (2300 miles) from its launch point near North Korea’s capital of Pyongyang.
The key word here is “over.” Like way over. Like 770 kilometers (475 miles) over Japan at the apogee of its flight path. Neither Japan nor the United States could have intercepted the missile. None of the theater ballistic missile defense weapons in existence can reach that high. It is hundreds of kilometers too high for the Aegis interceptors deployed on Navy ships off Japan. Even higher for the THAAD systems in South Korea and Guam. Way too high for the Patriot systems in Japan, which engage largely within the atmosphere.
http://www.defenseone.com/ideas/2017/09/no-we-cannot-shoot-down-north-koreas-missiles/141070/