Oh wow. This is going to be an interesting bug to figure out. Best guess so far is some kind of recursive rewarding of random points. I'll take a look at the code for the boss drones and see if I can find what caused this.
This happened again in my most recent playthrough. I think it's some sort of interplay between Combat and Science upgrades. I had to win the game quickly (in terms of real time) before the game lagged out completely.
I no longer have my choices of upgrades in front of me, but I think the relevant upgrades are as follows:
COMBAT > 2 random points per kill
COMBAT > "Beam Splitter"
COMBAT > -1 Defense needed per laser shot
SCIENCE > Destroying an enemy damages all other enemies (I think the Technology name used the word "Shrapnel", but I forget the entire name)
I was shooting only the Mothership, leaving the second shot from "Beam Splitter" to hit Local Threats.
Based on what was being animated, the points being awarded were arising from a recursive killing of Local Threats. The Local Threats "died" but weren't actually removed, damaged other Local Threats via Shrapnel, which then "died" (but weren't actually removed), then got "killed" by those other Local Threats via Shrapnel (but wasn't removed), damaged other Local Threats via Shrapnel, AD INFINITUM.