Married Filing Separately

According to Turbox Tax if you are filing Married Filing Separately you and your spouse must both itemize deductions.  We usually do this with no problem.  This time Turbo tax switched my wife's return to the standard deduction because it was the better option.  I have not filed yet.  Wont this raise a flag with the IRS if Turbo tax files our returns this way?  Can I decline the standard deduction in turbo tax to make sure my returns are not wrong?  Thanks.