Have set up a class for particular sales which have fees deducted from them, why are the fees added when I run a class report?

if the class is tagging a sale, that is income, income is always the gross amount

then you have expenses, the fees, which should not be part of the sale itself

If you want to see sales income less fee expenses, run a P&L and in customize set the report to only show those accounts, memorize it for future use