If the distribution passed through your hands (as opposed to a direct trustee-to-trustee rollover), the 1099-R you receive at year's end would correctly show a Distribution Code of "7" - normal distribution.
The Distribution Code for a direct trustee-to-trustee rollover would be "G".
When you enter a 1099-R with Distribution Code 7 into TurboTax, one of the follow-up questions will ask what you did with the money. If you did a 60-day rollover of all or part of the distribution, you'll be able to indicate that to the program, and be taxed (or not taxed) accordingly.
Code G is only for a rollover to or from a qualified retirement plan like a 401(k), not for any movement of funds between IRAs. A proper trustee-to-trustee transfer between like-kind IRAs is not reportable at all.
Since it appears that they have treated the movement of funds from one IRA to another as a distribution, you'll need to get them to correct their records to show it as a trustee-to-trustee transfer as long as the money was made payable to the new IRA instead of made payable to you personally. If the money was made payable to you, giving you constructive receipt of the funds, and you subsequently deposited that money into a new IRA, constituting a rollover, you have a problem because that distribution indeed included your RMD since the first amounts distributed are RMD until the RMD for that account is satisfied and RMDs are not eligible for rollover. Depositing an RMD into another IRA as a rollover constitutes an excess contribution to the receiving IRA and correcting that would require an explicit return of contribution before the due date of your tax return.
To summarize, it appears that you indeed have a situation that needs to be corrected. You should not wait until next year to correct this, do it now. Escalate to the financial institution's back-office IRA personnel.