The inventory_quantity field is the listed inventory for an individual variant record. Whereas the variants_inventory_count is the sum of inventory across all variants of a single product.
For example, let’s say I have a “Black Shirt” with variants/inventory:
Size S: 2
Size M: -3
Size L: 2
My variants_inventory_count would be a positive number for each record, but inventory_quantity would be -3 for my “M” variant.
However, a product with only 1 variant reporting its inventory_quantity in a negative number is not expected behavior, you may contact the Support team to verify the issue.