Not sure if this might be the cause, but: Click on "edit this person" for both Amelia and John and look at the relationship tab to make sure that John does not show up as a preferred spouse and also an alternative spouse for Amanda and then do the same with John. Also, check each of the children the same way to see if one or both of their parents are listed more than once from the same view (edit>relationships).

This does happen when their is a cousin marriage and it is not an error, although at first blush, that doesn't appear to be the case here.