Honestly, it just looks like they are slow growing and attracting algea on the older stems.
Most people top these and space them closely so they grow in a colorful bush.
As they get close to the light in your tank, the tops get more PAR and develop color. If you trim them short, they will get much less PAR and grow slowly. This is the nature of this plant, eventually after topping them several times, you have to start over because the original stem gets bad.
It looks to me like you don't have enough light for this plant, and they should be topped frequently to keep them in a bush so you are only seeing the exterior leaves.
The lower parts of the stems are probably many months old and if the tank is not 100% algae free, the old stems will attract algae.
I am keeping rotala with some success, but the old stems will eventually get this way. The solution? Top them frequently, plant them close, and run high light so they are always pushing out colorful new leaves on top.
Can you clarify what you mean by topping in this context? I've always understood this to mean cutting the tops and replanting them in place of the bottoms. But in my experience, replanting the tops prevents them from growing bushier, since additional nodes aren't generated from the clipping point of the original stem and the new growth on the topped (replanting trimming) stem is less bushy.