Just because some political General writes a stupid war plan doesn’t make it Top Secret or Classified.
Classification is one thing - the President can classify or declassify anything. But war plans are unquestionably national defense information, and Trump is charged with possessing and refusing to return national defense information, not with mishandling classified documents. Now it does not appear the Milley document is even the basis for one of the charges, but if it were, whether or not it was classified would be immaterial to the charge.