Happens to me to but I notice what causes this for me. When I do my first click it is over the enemy unit but the second click occurs after the army marches forward and the cursor is over another enemy unit or on the ground. Where I have my biggest problem is when I have 2 enemy units stacked on top of each other and the second click ends up on the other unit. My other problem is I slightly lag on my PC in the beginning of a big battle when misslefire is flying everywhere and this slight lag I get causes the monitor not to show the cursor in the proper location. Even if the cursor is off by a few milimeters this can make a big differance.

I can't explain cursor lag all that well but understand it quite well. Maybe some techie could explain it well if you do not understand what it is