The reason the song's has the Prince Charlie anachronistic reference is because it was a later romance of the 1715 rising long after Prince Charlie was gone.

  
         E
  The standard on the braes o' Mar
     A                   (7)
  Is up and streaming rarely, 
  The gath'ring pipe on Lochnagar
      B7                 E
  Is sounding loud and sairly,
  
  The Hieland men, frae hill and glen,
  Wi' belted plaids and glitterin blades,
        E               (C#m)
  Wi' bonnets blue, and hearts sae true,
      B7               E
  Are comin' late and early
  
        E                      A
  Our prince has made a noble vow,
      B7               E
  Tae free his country fairly,
                               A
  Then wha would be a traitor now,
      E      B7        E
  To ane we lo'e sae dearly, 
  
  We'll go, we'll go and seek the foe,
  By land or sea, wheree'er they be,
        E              (C#m)
  Then man to man, and in the van,
         A                 (F#m)
  We'll win or die for Charlie.
  Then man to man, and in the van,
         B7              E
  We'll win or die for Charlie.
  
  I saw our chief come o'er the hill,
  Wi' Drummond and Glengarry,
  And through the pass came brave Lochiel,
  Panmure and gallant Murray.
  Macdonald's men, Clanronald's men,
  McKenzie's men, McGilvray's men,
  Strathallan's men, the lowland men,
  O' Callander and Airley.

[Hogg notes that 'The earl of Mar erected the chevalier's standard there (at Castleton of Brae-Mar), on the 6th of September, 1715'. This began

the Jacobite rising of 1715, the 'fifteen'.]