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 warning is Advisory. It exists to encourage good practices and flag possible mistakes, but it isn’t a strict requirement to fix it.
Description
This warning appears when a document contains Parts, Chapters, cross-headings or other grouping headings, but not all of the clauses, sections or paragraphs in the document are included within those groupings.
Examples
The two screenshots below indicate document structures which would trigger this warning. In the first, Section 1 appears before the two Parts; in the second, Section 4 appears after Part 1 and before Part 2.

How to fix this document check
You can fix this document warning by moving provisions around using the Structure view, so that no neighbouring provisions are at different ‘levels’.
Steps
Go to the Structure View on the left-hand side of the screen;
Identify the provisions that are outside of their required locations, and the grouping provisions that they should be contained within (if there are none, see Creating new grouping provisions below);
Click on the first provision you need to move, so that it appears highlighted in bold;
Click again and drag it to the required location;
Repeat for all provisions that need to be moved;
The document warning should disappear.
See Moving provisions, tables and amendments within a document | Moving-using-the-structure-view for further detail.
You may want to renumber your provisions after you move them, as depending on whether you have ‘auto-renumbering’ active the numbering may change.
To renumber, see Renumbering provisions
Creating new grouping provisions
You may, alternatively, want to fix this issue by creating new grouping provisions.
For example, in the first example illustrated above, you might want to create a new Part for Section 1, instead of moving it to Part 1.
To do this, you have to ‘wrap’ the provision(s) in a grouping provision. See: Wrapping and unwrapping provisions
Demonstration video
The video linked below explains this document check and demonstrates how to fix it using an example.
Explanation
Documents drafted in Lawmaker are structured documents, in which provisions are contained within other provisions in a hierarchical structure.
Even if a document visually appears to be organised properly in the Editor or in the PDF version, it may not actually be organised hierarchically - for example, Regulations may appear to be organised in Parts, but actually they sit beside the Parts, on the same 'level', as in the examples above.
This is consequential because when the document is made law, it will be difficult for readers using computers to access information within the legislation; for example, readers would not be able to see what was contained in a Part, because the provisions meant to be contained within that Part are actually outside of it.