the_content doesn’t affect the DOCTYPE and <html> tags, only the post/page content.
One of your plugins, or something else in the theme is either throwing an error, or is printing something earlier than it should.
Have you tried:
- Disabling each plugin one by one and see when it is fixed.
- Editing wp-config.php and adding
define( 'WP_DEBUG', true );to look for errors
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