
The problem with ball play is twofold. One; it does indeed involve these sharp, sudden movements but also very high impact events - when the dog gets to the ball there's often a sharp stop as they pick it up, when the feet plant into the ground and you can see the judder through the whole body. That is massive impact on all the joints, very bad news for a growing skeleton. Two; repetition. These events are happening over and over, putting excess wear on those joints.
In puppy pla, not only is it often more gentle than the immense forces involved above (and I am making a mental note here to see if I can find any quantitative information on those for future use), but it's much more varied and not the same movement repeated again and again. Many more muscles are involved, so they're getting toned up nicely, and it improves coordination and balance. They can also stop if they are uncomfortable but ball chasing tends to bring in an element of obsession for most dogs, and they will keep running long past injury or discomfort. I've seen that happen many times, including with my own Phoebe in her last home - she had a soft tissue injury after she ran shoulder-first into an iron bench (chasing a ball, of course) and she continued to chase one despite being in obvious pain and with a bad limp (and despite me telling the owners to stop throwing it because she'd never heal otherwise and that leg can still be a problem today).
That obsession can lead to other problems too but that's behavioural rather than physical.