Please help on soft-rejected wordpress theme

Hello All,

Its my first wordpress theme here. TF suggested some improvements, I did. But I’m confused with these two things (cheked with Theme Check):

WARNING: The theme uses the add_shortcode() function. Custom post-content shortcodes are plugin-territory functionality.
REQUIRED: The theme uses the register_post_type() function, which is plugin-territory functionality.

This post-type and shortcode functions have been used in ACF plugin itself. Can I edit it? or will it work ? Now, what should i do ? I can’t get it. Please suggest.