That’s a constant issue he has, and his only real weakness. Kryptonite, depending on the writer, doesn’t hurt Superman, it just drains his solar powered plant battery. He doesn’t resist magic, but it doesn’t stop him.
Superman’s only real weakness is that he holds back. That’s it. He’s limitless, but limits himself to keep from breaking everything or solving everyone’s problems.
For an example of Superman not holding back, see Robin with superpowers in Teen Titans GO! (Why DC? WHY?!?)