Roth contributions spread across 2 years are a 2-step process. For the 2023 tax return, you should have prepared a Form 8606 - check your tax return to verify you did. If not, you can do so now. There may be a $50 late fee assessed unless you have cause. See: About Form 8606, Nondeductible IRAs to get a pdf form and fill it out, if needed.
Next, since the conversion for both years happened in 2024, it is correct that they were both reported to you on the 2024 1099-R. In order to ensure no tax is computed on the conversion, since you did not deduct them in the first place, after you enter the 1099-R, continue through the interview until you are asked if you moved the money through a rollover or conversion. Answer that you converted (all of it) to a Roth IRA. You should also report the nondeductible basis of prior year in this section (the 2023 contribution.) Separately, in Deductions, you'll report the 2024 non-deductible IRA contribution. This will endure the 8606 reports the 2023 nondeductible basis, the 2024 contribution, and subsequent rollover, leaving you with a $0 basis on Form 8606 at the end of 2024.
Here are the full instructions to report a Backdoor Roth: How do I enter a backdoor Roth IRA conversion?
