A magnet stone is a magnet. Magnets look like little stones, right?

The 磁 reading makes sense. The しゃく reading for 石 is an exception. To remember this, just think how you are using a magnet to find this shack (しゃく) full of other magnets. It pulls you towards the shack, and when you find it and open it, all the magnets fly out and crush you because of magnety reasons.