Yes I think you are missing something. Assuming that you have entered the relationships correctly, ie with cousins marrying you have merged them properly to reflect both relationships.
Have a careful look at the relationship report and in particular the middle bit with relationships.
If you have multiple relationships, there is an indication (number) of the number of the relationships and a drop-down to show the various relationships.
You may have missed both the number and the drop-down see the attachment.