It indeed seems to happen when something that has produced smoke particles goes on-rails and gets removed by the game. I tried a few simple tests with the Dev 12 version, version 2.0.1, as well as the version that HotRockets comes with, and they all generate the same NPE spam. Here's a log file and small example craft, hope it's of any use. https://www.dropbox.com/s/ewa04f10bfz0pve/KSP%20Testing.rar