When using Contact linking it is unclear in the pop up that you are choosing for both primary contact 1 and primary contact 2 regardless of which contact you are trying to link. For example, you are on primary contact 2 and you get the same pop up window as you do on primary contact 1, you might think you are only linking numbers for primary contact 2 and have the option to link two numbers for contact 2, when in reality you are overwriting your contact 1 selection if you put anything in the top box.