I edited the rootfolder/modules/gateway/Stripe/gateway.class.phpgateway file to solve the charge difference.
near line 113, change
$source = \Stripe\Source::create(array(
"amount" => $this->_basket['total']*100,
"currency" => strtolower($GLOBALS['config']->get('config', 'default_currency')),
to
$source = \Stripe\Source::create(array(
"amount" => $this->_basket['total']*1,
"currency" => strtolower($GLOBALS['config']->get('config', 'default_currency')),
and near line 130, change
$charge = \Stripe\Charge::create(array(
"customer" => $customer_id,
"amount" => $this->_basket['total']*100,
"currency" => strtolower($GLOBALS['config']->get('config', 'default_currency')),
to
$charge = \Stripe\Charge::create(array(
"customer" => $customer_id,
"amount" => $this->_basket['total']*1,
"currency" => strtolower($GLOBALS['config']->get('config', 'default_currency')),