The connectors of the shapes are located next to the edge of the Shapes(outside of the shape boundaries). That said the connector center to witch the connection is connected is not overlapping the shape border.
In order to make the center of the connector and the shape boundaries to overlap you should change the position of the connector itself. I have noticed that you are having custom connectors which are located at the angles of the shape and their position is ( 0 1 and 1 1). For instance if the border of the shape and the connection connector to it are 1px you should offset the position of the connector to (0 0.99) doing so the connection will overlap the edge of the shape.
I hope this information helps.
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