It’s not actually an error, it’s just not detecting that WooCommerce is activated. There are two possible reasons. Either way the plugin will work fine (assuming WooCommerce is active). Just navigate to settings -> WP Menu Cart Setup and set it up on the options page.
Here are the reasons you might get that message:
1. It’s part of a multisite install.
2. You don’t actually have WooCommerce enabled
3. Your WooCommerce install doesn’t look like the following: woocommerce/woocommerce.php.
Again, it’ll work fine if you have everything enabled properly. It’s just a message we setup because WordPress doesn’t detect that you have WooCommerce installed.