I am a 19 y/o freshman in college. I had two summer jobs and received a W2 & 1099-NEC. I contributed money from both to a Roth IRA. Turbotax is saying I over-contributed?

Yes you can use a 1099NEC but you have to fill out Schedule C and have a Net Profit.  A 1099NEC is for self employment income.

For an IRA contribution.  If you only have self-employment income you can only contribute up to your net profit reduced by the deduction allowed for one-half of your self-employment taxes then only up to the max IRA limit.

See IRS publication 590 http://www.irs.gov/pub/irs-pdf/p590a.pdf

So check 1040 Schedule 1 line 15.  You have to deduct that amount from your Schedule C Net Profit.  That will give you the allowed contribution for self employment & 1099NEC income.