My Home pages(index.php) are not being loaded by index.php, instead they are being loaded in page.php or single.php I'm not able to figure out the reason for this.
2 Answers
From Settings->Readings you have set a page as home page. If you set a home-page and blog-page form Settings->readings then home-page will show form page.php and blog will show from index.php. If you want a default and permanent structure for front-page/home-page you may set front-page.php, It will show on home-page. Thanks.
Comments
Check the WordPress hierarchy out. If you want it to load index.php you have to delete single.php for single posts and page.php for pages.