When building a stone wall, it's almost impossible to avoid getting mortar on the stones. If you try cleaning mortar off while it's still wet, it just smears on the stones. An easy solution is to let the mortar dry, and, at the end of the project, clean the mortar off the wall with muriatic acid.
The first step is to get the wall wet. Never apply muriatic acid to dry stones. If the stones are dry, the acid can stain them, turning them a yellowish-green color. Make sure the stones that you'll be cleaning mortar off of are completely soaked before you apply muriatic acid.