Could you be more specific as to the problem?

• Should Methodology be numbered 3.1 or 3?
• Should Methodological Framework be numbered 3.2 or 2?

Could you perhaps copy those two headings and a TOC into a sample document and attach it here?

• Attach a Sample File Demonstrating the Problem - Here's How

Here are a few resources.

• How to create numbered headings or outline numbering in Ribbon Versions of Word by Shauna Kelly
• How to create a table of contents in Microsoft Word by Shauna Kelly
• Preparing a Manuscript (Thesis) in Microsoft Word 2007 - pdf - Ohio University

Could you perhaps copy those two headings and a TOC into a sample document and attach it here?