You cloned your Magento from Github, so all your core is in folder app/code/Magento/, you need remove it and run the composer command to have your core in the folder vendor/.
Note that you shouldn't clone the repository, next time install using Composer.
These are the steps that I used to fix:
rm -rf var/view_preprocessed/ var/cache/ var/page_cache/ var/di/ var/tmp/ var/generation/ pub/static/frontend/ app/code/Magento/ vendor/magento composer.lock
chmod 777 -R *
composer update -vvvv
php -f bin/magento setup:static-content:deploy
find . -type d -exec chmod 775 {}
find . -type f -exec chmod 660 {}
chmod u+x bin/magento
bin/magento maintenance:disable
bin/magento cache:clean
The Composer command will install de vendor modules.
rm -rf var/cache var/generation var/page_cacheand also do you have a duplicate copy of Magento_CatalogInventory module in your app/code directory? – Loxzibit Jan 03 '17 at 21:05