Baby shaking is a criminal offense. Might want to change your post title.
You're baby trembling while stretching, is yes, just his nervous system developing. If he acts otherwise, like you can't disrupt the shaking or he appears a little zoned out during the trembling episodes, then yes, you have a problem.
If it helps to alleviate your concerns, then keep a log of frequency, where, when of when these tremblings occur. You could even video tape it to show at your next peds visit.
Both leg and lip trembling are very normal as they stretch and open.