IIRC correctly, the scout drone base defense mission crash comes from having no floor sprites for the smoke pellet ammo. When the base mission starts, it looks in stores and tries to generate a random amount of items from the stores in the General Stores modules.
There are two work arounds:
= tell it to use a different set of sprites for the pellets. (say incendiary auto-cannon clips, etc).
= revise the scout drone to be clipless or use infinite ammo.
This discussion is also in the scout drone thread, as well as a copy of my workaround. I used the latter method: infinite ammo, but I shortened the range to 3 tiles to replicate a defensive smoke tactic.