After numerous conversations with warranty/service/sales personnel, they insist its a stone chip. There is what may possibly be a stone chip, in my opinion it isn't, but they appear to have the upper hand. I spoke to my insurer who tells me it will cost me £75 for a replacement for them to replace it, without loss of no claims bonus. So I have given them the go ahead and its booked in for next Monday. I could have had it later this week but I am away for a few days.
Ford were saying if they repaired it it would be several weeks before they could get a replacement. I suspect at an enormous price.
So guys check your insurance, make sure you have glass cover. You may well need it if you have the sun roof.
Thanks for the replies