There are a few things that format checkers see a lot. This video shows some of these things and demonstrates how to fix:
• blank pages
• headers (inconsistent capitalization and centering, and headers at the bottom of a page)
• tables and figures (incorrect centering and capitalization, illegible tables and figures, captions on a different page, tables and figures that are more than one page long, and thesis file size that is too large because of a lot of image files)
• extra white space at the top and bottom of pages
• things that are out of place
• Table of Contents, List of Tables, List of Figures, and List of Appendices for correct headings and page numbers
• Arabic page numbers in the Table of Contents instead of Roman page numbers
Remember to check your thesis with the Master's Thesis Format Guidelines before you submit your thesis. That will help you get your thesis format approved faster.