I've figured it out the problem occours when
Product SKU = Y
Product Attribute SKU = Y
So the SKU of the product and the SKU of one of its product attibutes is the same
So this is in part a problem with our clients configuration
Although I suppose when inventory method = "Track By Product Attribute" the product SKU should be ignored
For clarity I have a file
SKU, Quantity
X, 10
Y, 20
Item X is imported with quanity 10 if inventory method in "Track Inventory"
Item Y is not imported its inventory method is "Track Inventory With Product Attributes"
The plugin is not working when the inventory method is 'Track Inventory By Product Attributes'. Is there a bug?