No, they only report this at gross distribution amount. Truly, I have not seen/heard of your particular situation so I am curious....when you state "my excess contribution resulted in a loss and the amount sent back to me was less than I had excess contributed" - It appears as though for that year the IRS already calculated the net difference. However, you can check this by retrieving your transcript for that year and see what the IRS has with respect to this 1099-R.
IRS - Get My Transcript
If what they have is what actually happened, then the information has already been adjusted, which is why you received less than expected back. Any other/further questions/elaborations on this, please ask! I would be more than happy to look further into this should you need me to.
