An update for anyone else having this issue, The issue turned out to be that the Magento 2 Extension attempts to create a Stock Item, because the product has already been saved (Which creates a stock item) the extensions is unable to create a new one due to duplicates, Instead what should happen is after a product is saved it should load the existing stock item and modify it as required.
The offending can can be found here:
and can be fixed by replacing the createStockItem function with the following code
private function createStockItem()
/** @var $stockItem \Magento\CatalogInventory\Model\Stock\Item */
$stockItem = $this->stockRegistry->getStockItem($this->product->getId());
hope this helps you.