For the odd numbering you are seeing, it looks as though the text is formatted as bullets (it is possible for bullet formatting to exist when it’s not visible). Select the text and go to Format > Lists > None.
That depends on what format you are exporting to. Are you creating a PDF file? If so, select the documents you want in the ToC and use Edit > Copy Special > Copy Documents As ToC, then paste into the document in which you want your ToC. The current version doesn’t support internal links in PDF files, so you will need the beta of the upcoming version for this to work, available here: