Sounds like you had a case with some debris on it, or embedded in the case walls. I see it frequently with brass that has been stepped on, on concrete or gravel; or ejected onto crushed gravel.
If the scratches are not too deep, you may be able to polish them out. But, it may take a bit of work, and will increase the internal dimensions in the die.
The better choice would be to contact the manufacturer, and see if they'll replace it.
"Such is the strange way that man works -- first he virtually destroys a species and then does everything in his power to restore it."