I'm seeing the same thing, or at least something similar, on a game started with the latest patch.  It's happened 3 times so far, each time when attacking a mining base on asteroids with a fleet with mixed weapons, at least one of each type.  The quick battle animation starts playing, and I see (1) what appear to be beams flashing from my fleet to the base, (2) what appear to be missiles flying from my fleet to the base, and then (3) nothing happens for a long long time until finally I see what appear to be a kinetic attack flying from somewhere from the bottom left of the screen (perhaps coordinates (0,0)?) to the mining base, finally destroying it.

Most of the time, the kinetic attack (3) appears normally, originating at my fleet and hitting the asteroid base, but like I said, so far in this game it's happened 3 times that they appear to come out of deep space instead of from my fleet.

I'm playing as the Terrans in the Arcean campaign, so if this is the same problem that @corgatag reported it has nothing to do with the Snathi.

I saw this again, in another campaign map, on 1.81.  The map was medium this time, so the wait was much much longer.  Otherwise, identical to what I described in my post above.