My stone is oval shaped as viewed from the side. When you watch it rotate it rises and falls with the oval high and low areas. Why, and does that require truing? It has no bearing on my ability to sharpen a knife.
It happens normally. Freehand sharpening encourages it more than using jigs, but it is still normal, either way. The longer you let it go, the more pronounced it will become. I wouldn't be too concerned, but when you notice it, it is generally a good idea to true the wheel.