No, there is not a glitch in the system. For some states even though you used the Standard Deduction for the Federal it is to your benefit to take Itemized Deductions for your state return.
States use a different amount as a Standard Deduction than the Federal uses.
By taking Itemized Deductions for your state it reduces your tax liability since the Itemized Deduction amount is greater than the Standard Deduction amount for your state.