In looking at the two images that you posted with your original message, it appears that you have not properly attached Nehemiah. If you look at the the bar in the family view above Nehemiah, It says "Add Parents" If it were me I would look at adding William again to Nehemiah.
I have had the most success in situation like this by going to Person, Family for Nehemiah. Highlight Nehemiah, and from the Menu (File, Edit, View, ..................), Click Person and select "Attach/Detach Person" This will give you several combination of people to add to Nehemiah. Select Father and it will give you the index, Scroll down to William and highlight him and Click OK
If this does not correct the problem try the following
When you look at William in People, Family.
Does Hubert and Nehemiah show up as his children?
When you say 'tree' view" exactly where are you seeing this.
In People, Family in the top middle pane?
If you look you look at William in a report. ie Publish, Relationship Reports, Family Group Sheet.
Do you see both Hubert and Nehemiah