1. Ensure the variants are in the feed file and mapped correctly
Please check the feed file that you received from the supplier, is that provided the products with variants or not. If the variants are present, then make sure to correctly map. Click here to know more about variants and product identifiers.
2. SKU no longer exists in feed data and quantity remains as it is.
To avoid selling SKUs that no longer exist in the feed file. You can use it to reset the quantity as zero. Click here to know more.
3. Wrong location
Please ensure that you selected the correct location before updating the products. If selected a different location then it will be updated in another location's products. Click here to learn more. 
4. Multiple products with the same product identifier
If you have multiple products with the same product identifier, you can enable it so that the update won't overwrite each other. Click here to know more.
5. Shopify Track inventory
Enable the "Track quantity (Set up inventory tracking for the products)" It will help to set all the updating variants to track the Shopify product's inventory.
6. Quantity Rules
Please ensure that the quantity rules that you entered are correct as it could affect the stock level. You can find the quantity rules in the quantity field's more setting.
7. Frequency of update
Sometimes the frequency of updates could cause the wrong stock update when it runs at the wrong time where the stock level is updated from the old feed. So, you also should check if is there got duplicated feed.
8. Use the highest quantity value when the same SKU detected from multiple feeds
When you have the same SKU from multiple feeds, it could cause the stock level to be updated based on the latest update. Enable the option to use the highest value, this option only can enable by contacting the support team. You can see this option under Preferences > Advance. Click here to know more. 
9. Filter - Exclude
Please ensure that the product is not excluded from the update. You can do this by specifying the products in the filter section. Those products that are excluded from the filter, it will cause the product not to be updated.
10. Add or deduct option in Quantity more settings enabled
Stock Sync will replace the stock value by default. You can choose to add or deduct the stock level with these options. You can find the add or deduct option in the quantity field's more setting.