extrudeMesh - odd behaviour
 

I have a mesh in with snappy in which I refine around a pipe cross-section and a stl surface a the bottom. I then convert that into a 2D snappyHexMesh, so I run extrudeMesh. This step works well sometimes, but sometimes, i get odd behaviour at the bottom where it just creates an outlier point. this point is not there after snappyHexMesh runs. extrudeMesh creates this for some reason i can't explain. As i said, sometimes it works ok then with a slightly changed bottom stl it won't and the odd points might occur in a different place (see images). The bottom stl is created using the constantIso sampling tool in sampleDict if that makes any difference. Has anyone experienced this before? what could be the issue? the hex-meshing step always works ok, the extrusion seems to be an issue.