How to remove panel-separator CSS in mini-panels?
All you need is to override the panels_default_style_render_region function.


Open your template.php file that can be found here:
/sites/all/themes/YOURTHEME/
Create a  new function in end of the file 

function YOURTHEME_panels_default_style_render_region($vars) {
    $output = '';
    $output .= implode('', $vars['panes']);
    return $output;
}