When the selected component is behind the mesh and PolyPen is making a knife cut that is not a loop cut, the cut will snap to all occluded verts as well.
The best solution in this case would be to connect the shortest path between the two points rather than make the cut in screen space.
Blender's own knife can't do this, so it's not a high priority. In the meantime, it may be worthwhile to block PolyPen from creating a cut if the selection is occluded.
When the selected component is behind the mesh and PolyPen is making a knife cut that is not a loop cut, the cut will snap to all occluded verts as well.
The best solution in this case would be to connect the shortest path between the two points rather than make the cut in screen space.
Blender's own knife can't do this, so it's not a high priority. In the meantime, it may be worthwhile to block PolyPen from creating a cut if the selection is occluded.