apply_filters is a function used all throughout WP in many different contexts, your issue here is the specific filter you are applying, which is the_content.
the_content filter by default runs on the main post content field, and does all sorts of transformations via a number of hooked functions: wptexturize, convert_smilies, wpautop, do_shortcode, shortcode_unautop, prepend_attachment, wp_make_content_images_responsive.
In your case, the markup is an embed automatically generated by WordPress when an embeddable URL is encountered within the content.
It doesn’t make sense to use the_content filter in the case of your URL field, you should just use esc_url instead:
echo '<a href="' . esc_url( $ecpt_website ) . '" target="_blank">';