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:
vendor/m2epro/magento2-extension/Model/Magento/Product/Builder.php
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());
$stockItem
->setQty($this->getQty())
->setIsInStock(true)
->setUseConfigBackorders(true);
$this->stockRegistry->updateStockItemBySku($this->product->getSku(), $stockItem);
}
hope this helps you.