I don't know exactly what makes TurboTax report a transaction on Form 8949 instead of Schedule D line 1a. But since the totals are correct it appears that your tax return is correct. Using Schedule D line 1a is an option, not a requirement. The IRS is not going to complain about transactions on Form 8949 that could have been included in Schedule D line 1a.
Do the transactions that are shown on Form 8949 have adjustment codes in column (f)? If so, they have to be on Form 8949. They cannot be included in Schedule D line 1a.
