It's a bug in Magento 2 already fixed in develop.
All query results to tables store, store_group, store_websites are being cached. The problem occurs because cache isn't cleaned properly after store, store group or website is added/deleted.
SeeTo get a fix see changes to app\Magento\Store\etc\di.xml in next commitapp/code/Magento/Store/etc/di.xml and app/code/Magento/Store/Model/StoreManager.php.
It must resolve the issue.