No, overriding an entry will not trigger an audit, but it will prevent you from e-filing your tax return.
You may be interested to know that the IRS drops the cents off all figures to avoid getting lots of discrepancies due to rounding errors. So, if your 1099-B says $6,641.72 as your total adjustments and your Schedule D lists $6,641 as the total adjustments, that will match as far as the IRS is concerned.
If you feel you really need to match the $6,642 figure exactly, you can just round one of your line 1g entries up instead of down.