Without seeing your show_sticky_posts, show_lastest_posts, show_lastest_missions,show_all_posts_from_categories
i can guess that the shortcode content is always before the post content beacuse this functions are echoing/outputing the result and a shortcode should return content instead so you can try using output buffer of PHP like this:
function show_posts_handler( $atts, $content=null, $code="" ) {
//code 4 displaying
extract( shortcode_atts( array(
'sticky' => 'false',
'latest' => 'false',
'missions' => 'false',
'count' => '0',
), $atts ) );
ob_start();
if($sticky != 'false'){
show_sticky_posts();
} else if($latest != 'false'){
show_lastest_posts($count);
}else if($missions != 'false'){
show_lastest_missions($count);
}else{
show_all_posts_from_categories();
}
$output_string = ob_get_contents();
ob_end_clean();
return $output_string;
}
add_shortcode( 'show_posts', 'show_posts_handler' );