The negative pressure will have caused this, it also happened a couple of times on aircraft with the earlier Everests. The earlier ones had the crystal fitted by compressing it with a crystal tool and then placing it in the case where it returned to the original size once released and this held it in place (usually). The later ones don't do this and the sapphire ones are fitted completely differently. If you've got the crystal, you can safely pop it back in.
Eddie