Using .htaccess and DokuWiki's own auth system is a bad idea. DokuWiki will try to use the external (.htaccess) login to authenticate you. This is quite handy when using an external auth backend as it allows SSO with Apache auth. In your case I recommend not doing that. Either disable ACL or .htaccess basic auth.
If this is for whatever reason not an option, remove these lines from inc/auth.php:
// if no credentials were given try to use HTTP auth (for SSO)
if(empty($_REQUEST['u']) && empty($_COOKIE[DOKU_COOKIE]) && !empty($_SERVER['PHP_AUTH_USER'])){
$_REQUEST['u'] = $_SERVER['PHP_AUTH_USER'];
$_REQUEST['p'] = $_SERVER['PHP_AUTH_PW'];
}