Except in certain cases where you received a distribution from an inherited IRA. TurboTax determines the MAGI for the purpose of a Roth IRA contribution correctly as long as you enter the Form 1099-R for the conversion correctly. Even in the case where a distribution from an inherited IRA is involved, TurboTax never calculates a MAGI that is higher than the correct amount.
Be aware that if you did an In-plan Roth Rollover, taxably moving fund from the traditional account in an employer plan like a 401(k) to the designated Roth account in that same plan, this is not a Roth conversion that is excludible from the MAGI for the purpose of a Roth IRA contribution.
Even if the return of contribution was ultimately not to correct an excess contribution, the return of contribution was still a permissible distribution. The only part of the distribution that is taxable is the earnings attributable to the amount being returned, an you, not TurboTax, is responsible for ordinary income tax. TurboTax would only be responsible for interest and penalties due to a calculation error made by TurboTax, and there is no calculation error that resulted in you paying any interest or penalty.
