As you are in doubt about the print layout, the first thing to do is create a duplicate of the layout and work on that. Just right click it.
In the second page of the wizard you can also view topics by folder and the colour of the icon tells you whether or not a topic is in the document.
I would have thought two topics with the same title in the same book is a bit unlikely and is an error but only you can check that.
It looks like you need to rework those lists. You have a list that runs 1, 2, 3 albeit with the 3 outdented. You could try right clicking and restarting numbering.
You haven't said what version of RoboHelp you are using.
See www.grainge.org for RoboHelp and Authoring tips
I have a similar problem - but more limited
. All headings that are the start of a tree are duplicated. I think someone (perhaps Peter Grainge) posted a reply about 'books' in the TOC - I need more detail about that solution, as I cant find it again. Anyone able to help?