We will wait for a more authoritative response, but I believe the issuance to the 1099-R is correct and that it is up to you to report the information correctly on your tax return.
Had you just made a $12,000 RMD of which $2,000 was a QCD, the investment company is correct in issuing you a 1099-R for $12,000. You would have to account for $2,000 of the distribution being a QCD by reducing the taxable amount of the distribution to $10,000 and showing a notation on the return for line 4b and being a QCD.
I believe with the issuance of a $14,000 1099-R you would basically do the same thing and reduce the taxable amount on line 4b to $10,000 and have two notations; one for a QCD and one for a roll-over. The investment company is correct in the issuance of their 1099-R.
I am not sure what would be done, if anything, if you have already had a roll-over in the past year. Maybe Alan S. or someone else with comment on this matter and my post in general.