I keep getting the message that my Roth contribution was too high for 2018. However, I contributed $5,500 (the max) and converted $6,500 of traditional IRA to roth IRA.

Your activity seems to be appropriate and shouldn't generate a penalty if you enter the data for your traditional IRA conversion in the "Wages & Income" section of Turbo Tax and not in the "Deductions & Credits" section of Turbo Tax.  Refer to IRS Publication 590-A, Chapter 2, page 43 which states "excess contributions to a Roth IRA are not generated by amounts converted from a traditional IRA".  IRS Publication is available at www.IRS.gov.