The Problem

It seems that you're using the normal theme template files for posts and pages to display your custom post type. This means, that you also got the wp_head() hook and other template, that output default (post/page specific) things.

The solution

Add a template file to your theme, that's named single-{$post_type}.php and nothing than the loop with only the_content() in it. This way you can build your HTML without any interference.

The Problem

It seems that you're using the normal theme template files for posts and pages to display your custom post type. This means, that you also got the wp_head() hook and other template, that output default (post/page specific) things.

The solution

Add a template file to your theme, that's named single-{$post_type}.php and nothing than the loop with only echo get_the_content() in it. This way you can build your HTML without any interference.

get_the_content() has no filters applied, that normally get attached to the_content().