Whats this?! Anomalous intercept with big, armored missile.

I have built a big, warheadless, armored missile in order to experiment with anti-kinetic armor schemes. I have deployed it around Europa (the asteroid) against a Corsair. I went for intercept. The autointercept made a bad intercept, with flyby coming in 55 hours, and my ship speeding 'sideways' with about 1.4 km/s. I oriented the missile 'nose forward', and waited. My armor survived the few shots the enemy had the time to fire, so after it said 'enemies are moving away', I have decided, that the experiment was concluded, and went back to orbital view.

However, I have noticed that there is remaining dV, and a 'can intercept' marker at 0s. I clicked at it, barely noticed the 'pm/s' and micrometer values in intercept details, and hit 'Run Turn'. Then shit happened:


 As you can see, my missile is fully intact, and had buried itself into the enemy ship. After I unpaused , it was destroyed, while causing light damage to the Corsair.
I could replicate this thing one more time, and at the third time, I got this on the first intercept. Since in the meanwhile I have built in the stock 2MT nuke into the missile, I could punch a fairly big hole into the corsair. 

What is the cause of this?

(What program do you use to view text data files of the game?)

EDIT: I could replicate this on a gunship, and tear it half with more internal nuking, but never around other celestials.