I had a similar problem. First I needed to click at the top of the bag in my inventory. Then move my inventory window to the right because it opened under the inventory window. Then I added the gem that I had into the bag. It looked like it would hold 7 gems. I could be incorrect on the quantity.

Hope this helps.
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God grant me the serenity to accept the things I cannot change, courage to change the things I can and the wisdom to hide the bodies of those I had to kill, because they pissed me off.