I have double first cousins in my tree. I am not sure what your question is but will attempt to answer. The only was to avoid having them in your tree 2 times is to check each name before you enter them but it may still happen.
If you have these people in your tree twice you can merge them. I start with the parents and then merge the children. The people will only be in your tree once but will show up on both lines in the tree.
Hope this helps.