My 1099-R form box 9a from Vanguard says 0%, but Turbo Tax says says minimum value for this box is 0.01%.

You should leave box 9a blank if it has 0% on your Form 1099-R.  A blank entry gets read as zero entry but if you try to enter any value the program is going to want a minimum of 0.01%.  For your reference, this is true of most entries in TurboTax - unless the box specifically says you should enter zeros, then you should leave any boxes that have zero values as blank.