Yes indeed, nice to see a new mission, and with source up on GitHub. :)
I checked briefly into the SetEMPMissile code. I didn't see anything obvious that might cause that.
The unknown parameter 3 should be creatorIndex in:
static void __fastcall SetEMPMissile(int launchTileX, int launchTileY, int setToZero, int destTileX, int destTileY); // Set third param to 0
Apparently the "setToZero" name is indicating player 0 should own the missile. Maybe try setting that parameter to the AI player number.