Sometimes records do not make the family structure obvious. Sometimes it is difficult to figure out which mother is the mother of what children when the father has had more than one wife. Sometimes it is not immediately known who are the children of which father.
In cases such as these, before putting the relationships in your database, sketch them out on paper in an attempt to get things straight. Or, write up the information in a word processing document. There are families where putting the family structure in your database may simply have to wait.