We struggled with importing inventory changes in Magento 1; the issue was resolved when we started using OpenOffice spreadsheets instead of Excel. Our Magento 2 store doesn't seem to like Excel either, and OpenOffice works perfectly.
Make sure you have the column headers right, they must be exactly as Magento has them (sku, not SKU, etc).
Create the spreadsheet using only the columns you need to update (of course, the first column will be sku, even though you're not updating the SKUs). If you're unsure of the column headers, you can export your current item list (System > Export). Again, the headers on your spreadsheet must be exactly as Magento has them.
Populate the columns with appropriate data, but no formatting. Save as file type "Text CSV", name it whatever you want. In the "Field Options" window that pops up:
- Character set is Unicode UTF-8
- Field delimiter is ,
- Text delimiter is "
This may help you avoid issues. Once you get it working it's cake, and you'll be glad you did because it makes updating inventory much faster and simpler!