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I seem to have found a solution that's working at least so far. I'm creating two vertices on the shared boundary of the outer polygons and then snapping the inner polygons to that.


Unfortunately, you cannot save the dangles ends resultant from the topology checker into a new point shapefile since the points do not have any x,y locations and there is no option to turn the dangles into point shapefile. Hoping that someone can develop such an option to save the output of topology checker into a vector file.


Project polygons Add geometry attributes, inside centroids coordinates and convert to points to store attributes Convert polygons to polylines and simplify them. Build polygons and transfer attributes using spatial join


Well I just figured it out by myself a few minutes after posting this question. The solution is to set 'on-the-fly' transformation CRS so that it matches CRS of the shapefile. I assume it has something to do with transformation and floating point inaccuracy.

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