This may be the case of your stock levels having gone off-sync at some point in the past (due to connectivity issues, an incomplete bulk update, running a previous Magento version, etc).
In this case, you would normally do Inventory Taking to update the stock in Megaventory and that would bring all other connected Magento stores up-to-date too.
Although this is an option you can also make a less intrusive change which will automatically update the stock to the correct levels. In particular:
a. If you have more than one Magento eshop connected to your Megaventory account, you can update the Stock Alert levels in the On-Hand Inventory Screen and Alerts. This will update the stock levels to the correct (Megaventory) values in *all* the connected Magento eshops. Note that in the case of too many products to be updated you can also Import the Stock Levels via spreadsheet. This will update the stock in bulk.
b. If you have just one Magento eshop or want only specific Magento eshops to get the updated stock, you can click the 'Import Inventory from Megaventory' button located in your Magento backend in the Megaventory section.
In any case, the stock will be up-to-date after the above actions and will remain so with every order as specified by the extension functionality.
Note that this is a one-off action! You will not need to repeat it - unless your stock goes out of sync again for some external reason.