Details
Use the Stink Bomb at the Skitter Nest to smoke out the remaining Skitter.
Description
If their nest is as advanced as you say it is, their queen is already underground. This Stink Bomb ought to pacify those Skitter we can't easy reach.
Requirements
Progress
This looks like the right location.
Completion
Dropping the stink bomb in to the skitter nest you faintly here the cry of skitter deep beneath the ground.