Focus breathing is a lens behavior: as you change focus, the magnification/framing changes. For deep macro stacks, that can make alignment difficult.

Based on the answers, there are two practical options:

1. Use a lens with less focus breathing. Some lenses breathe less than others, but no general rule here says internal focusing makes a macro lens immune.
2. Keep the lens focus fixed and move the entire camera through the focus range instead. A focusing rail is the usual way to do this in macro work. That keeps magnification more consistent across the stack.

The tradeoff with moving the camera is perspective shift, which can also complicate stacking, especially on very deep subjects. In practice, this method is often preferable for macro because it avoids the framing changes caused by lens refocusing.

So yes, there is a solution: either choose a lens that breathes less, or stack by moving the camera rather than refocusing the lens.