Thanks for writing. Without being able to see your geraniums in person, I can't say for sure what the problem is.
There's a problem called oedema that's fairly common on geraniums; when they get more moisture than they need, their cells rupture. When this happens, they develop weak points on their stems or tan bumps on their leaves.
If the look of the stems bothers you, you could take cuttings from your geranium plants and start new plants.
Senior Garden Editor, BHG.com
Better Homes and Gardens