The body of the document is not divided into an even hierarchical structure. This is because not all provisions in the body are wrapped in the same kind of grouping provision (e.g. a Part).
This is an advisory warning which appears when a document contains Parts, Chapters, cross-headings or other grouping headings, and not all of the clauses, sections or paragraphs in the document are included within those groupings.
To investigate the cause of this message, look at the Structure View on the left-hand side of the Editor window. The two screenshots below show document structures which would trigger this warning. Note that the relative indentation of the section numbers and titles in the Structure View indicates whether the section is within or without the preceding Part. In the first, Section 1 appears before the two Parts; in the second, Section 4 appears after Part 1 and before Part 2.
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This type of document structure is sometimes intentional; where that is the case, the advisory warning can be ignored. If the intention is to include all sections under Part, Chapter, or cross-headings, and a section has simply become misplaced within the document structure, you can correct this by dragging and dropping individual provisions within the Structure View into position inside the relevant grouping headings.
There are two lists back-to-back when there should only be a single list containing multiple items. To fix, cut and paste all the items into one list and then delete the empty list.