The crystal bag is just ending up behind the inventory window when you click to try to drag and drop a crystal. Click and hold the crystal bag window to move it off to the side first, so it is not overlapping the inventory window, then you can transfer crystals back and forth. If you are playing at a low resolution and don't have much room, you can move the inventory partly off screen first, or put the crystals in a chest/barrel, so you can open the container inventory and the crystal bag windows on top of the inventory window, and drag and drop between them.
Welcome to the forum.
Stabbey;
There is a crystal bag in Beyond Divinity that can hold crystals, which boost resistances; Rayjfpr2 just posted in the Divine Divinity forum by mistake (or didn't notice the separate BD forums).
