Waffle weave is just the name of the shape. I have a microfibre waffle weave drying cloth. Waffle weave shape is better suited at drying, because it has small pockets, where water can be trapped during drying process.
There are good and bad quality waffle weave cloths. Just like there are good and bad quality microfibre cloths.
There are other waffle weave cloths as well, which may not be microfibre or may be a cheaper "blend" of microfibre.
So in short, swirl marks can be caused if a cheaper quality waffle weave cloth is being used.