You must verify a document's logical reading order manually. To check a document's reading order, open the Accessibility panel and select the Reading Order tool. In the dialog box, make sure the Show page content groups box is checked, and select the Page content order radio button below it. Each piece of content should be numbered according to its placement in the reading order. 

If content is out of order, use the Reading Order tool to modify the reading order. Select the Show Order Panel button to open the Order Panel on the left-hand side of the window. Here, you can drag and drop content items into a logical order.

A user edits a PDF's reading order in the Order Panel using Adobe Acrobat Pro's Reading Order tool.

WCAG requirement: 1.3.2 Meaningful Sequence