Hello there!
Im currently doing the tutorial on the bolt primitive in the prac guide and something strangeO is afoot…
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I recommend that you upload your images directly to ZBC rather than hosting them someplace else. It’s the only way to prevent things like what happened to your post.
cheers aurick, didnt realise it went all wonky 
Masking has NOTHING to do with polygons. It is 100% based on points. But because ZBrush can’t display a point itself as being masked or unmasked it colors the adjacent polygons to show that the point is masked. Deformations also do not affect polygons; they affect points and then the polygons formed by those points go along for the ride.
The problem that you ran into was that you changed your masking to get what looked right to you, but in the process you unmasked some points that actually needed to be masked in order to get the right results from the deformation.