I know this is an old question but I was having the same issue in a theme I inherited and came across this question in my search for answers.
In my particular case, I found the following PHP code included in the theme’s function.php
file:
if( is_category() || is_date() || is_author() ) {
global $wp_query;
$wp_query->set_404(); //set to 404 not found page
}
This code redirects any category, date, or author archive page to a 404 error (which brings up your 404 theme template). You may want to search for something similar in your theme (assuming you haven’t already figured this out).
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