In this example, we don't allow connectors to attach to nodes. Only ports.

Problem 1: The connector appears at (0,0) if you don't specify a source or target position. When you move a node, it'll show in the right place.

Problem 2: Delete the existing connector. Drag from the lower node's left port up to the upper node. If you don't drag the target end of the connector over one of the upper node's ports, the connector still shows that it is connected to the port.
When you let go of the mouse, the connector will go from the lower node's port to the upper node's port, however the connector won't be attached to the upper node. If you move the upper node, you'll see it isn't connected to the connector.
The image below is a screenshot of me doing this.