wordpress plugin | short code issue

Without seeing your code it is impossible to be sure, but my guess is that you’re echoing the output of your shortcode instead of returning it.

function my_shortcode($atts){
    //do shortcode logic
    echo $result; //This is wrong and would do what you describe.
}

function my_shortcode($atts){
    //do shortcode logic
    return $result; //This is what you should do instead.
}

If you have to echo within the plugin you can do this.

function my_shortcode($atts){
    ob_start();
    //do shortcode logic
    return ob_get_clean();
}

That function will store all your echo to the output buffer and then return that buffer as a string.