This is often due to unclosed or extra tags – validating your site may help find those.
http://validator.w3.org/
http://jigsaw.w3.org/css-validator/
Are you modifying theme files? That’s not a good way to go – as changes will be overwritten when the theme is updated.
You should be using a child theme to make changes –
http://codex.wordpress.org/Child_Themes