How to control whether a connection dot appears in the Quartus Prime Block Diagram editor?
The dots indicate two wires joining where they overlap. The reason they are appearing over some of the pins of the modules is that you're drawing the wires to far. 

The wires should end at the boundary of the module box (that is where the connection point is). By extending them further than this the dots appear indicating that the signal splits (there are two wires and a pin all converging at a point).

You can see that they have gone too far by the little x's appearing on the end of the wire showing that small section of wire doesn't connect anywhere.