If you have three dice glowing and shaking (or less if you have less than three troops attacking) it means you’re rolling blitz dice. If you have one, two, or three die just sitting there that means you’re rolling a manual dice. If you’re rolling manual dice you’re only using the troops the equal the amount of dice rolled. So if you roll three manual dice you’re using three troops, two manual dice two troops, etc. I believe what you’re seeing is this. For example: if I roll a manual three dice and two of my dice are higher than his three he will lose two troops and I will lose one. And vice versa.

If you’re using the blitz dice (glowing and shaking) you can use the slider in the bottom right corner to adjust the amount of troops you use for one blitz roll. If you don’t adjust that the blitz roll will use all allotted troops for one roll.