Known bug.

Multiple players suffer from this same issue on different difficulties (hardcore characters included).

After destroying the missile:
Keener defender drone is not present but protects him. It's impossible to disable the drone by standard methods and thus renders Keener unbeatable by usual means.
This bug seems to occur randomly but is quite frequent.

Multiple reports on Reddit.

Recent example: https://www.reddit.com/r/thedivision...till_an_issue/