I wouldn't conclude that the subcontractor has invoiced the VAT in the wrong way with the information you have provided so far. I understand from your post that your client is the contractor so I won't expect the subcontractor's invoice to include any CIS deduction element. It's the contractor (or contractor's bookkeeper) who will need to work out the CIS deductions based on what is included on the invoice. For example, is VAT, equipment or materials included? What makes up the 'Invoice for work completed £2800'?
It is quite common for sub-contractors to state the CIS deduction expected on their invoices in my experience. Although, as you rightly say, this isn't their responsibility they do so to reduce errors, delays in their payments & to aid their own record keeping.
Karen's example shows that VAT is calculated on the invoice value after the deduction of CIS, VAT however should be calculated before CIS deduction
You are quite right of course that not all elements may be vatable and perhaps the invoice value includes some elements that may not be liable for CIS deduction but if as Karen has stated, the figures are taken from an invoice provided then the VAT has incorrectly been calculated after deducting CIS
Karen, are you sorted now with this issue?