I was able to reproduce this, but not the way the original poster did. I found that if the rotor was moving on a MH9/AH9 and you drop _any_ weapon into the chopper it will take damage. I tried with the SDAR, a MX, P07 and the NLAW. Same result if I was the pilot jumped out and placed a weapon before the rotor stops, or if the AI was piloting and I was a passenger.