This is because in the higher sections, you are having a two-digit number (10 and above). You can solve this by adjusting the width of the hanging indent of your paragraphs. Select all your paragraphs. Right-click and choose Paragraph... from the short-cut menu. In the Indentation section of the Paragraph dialog box, increase the amount of hanging indent until you see all the paragraphs lining up properly. That should solve your problem.
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