Problem with Apply Filters on URL in meta box filed of custom port type

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">';

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