No, the user system does not have a trash (this is the default, obviously you can add pretty anything).
My problem was caused by users meta… If you take a look at the the function count_users (located in wp-includes/user.php), you’ll see some comments there. It says that the function:
- Assumes there are neither duplicated nor orphaned capabilities meta_values.
- Assumes role names are unique phrases.
In my case, there were orphan meta values. Deleting from wp_usermeta values having a user_id not present in wp_users table solved the problem.
Delete can be performed with a mysql query like this
DELETE FROM wp_usermeta
WHERE NOT EXISTS (
SELECT * FROM wp_users
WHERE wp_usermeta.user_id = wp_users.ID
)