The error usually appears for configurable products, when an Item Specific (e.g. Size) is also presented as an option in variations. There is no value for a custom attribute in the configurable product as all values are kept in the associated simple products.
So to avoid this error, all Item Specifics should be set not from Custom Attribute, but as Custom Value. You can put it as some generic info (i.e. varies, L-M-XL, etc).