I've created a custom content.php and removed any comments on the content.php page
then i changed the sharing-service.php from jetpack and added comments_popup_link there:
// Wrapper
$sharing_content .= '<div class="sharedaddy sd-sharing-enabled">';
$sharing_content .= '<div class="robots-nocontent sd-block sd-social sd-social-' . $global['button_style'] . ' sd-sharing">';
if ( $global['sharing_label'] != '' )
$sharing_content .= '<h3 class="sd-title">'. comments_popup_link( __( 'Leave a reply', 'changed2012' ) , __( '1 Reply', 'changed2012' ), __( '% Replies', 'changed2012' ) ) . $global['sharing_label'] . '</h3>';
$sharing_content .= '<div class="sd-content"><ul>';
and it looks like this:

does anyone have an idea why its getting moved there? and how i can move it back where it should be?

comments_popup_link()prints the result, and can therefore not be used in a string concatenation. I am not aware of an equivalent function to return a similar output. – Michael Jan 13 at 13:06