This has been really annoying me and cost me couple alien levels already on my fixer (nermindgrid):
I keep getting the mission to terminate the alien cocoons very often on him (ironically), but 4 (!) last times the alien handler doesn't give me the termination tool (he did only the first time), AND its not buyable in the Agency shop, makes me sad not to be able to do such an easy mission so many times, petitions take too long - by the time I would get help the next day maybe I would have lost a chance of rolling the next mission anyway.
Don't know what exactly caused this since I don't see this reported yet.