Noticed this same problem in Xcode 12.4 also. A workaround that works for me: Click on the custom color to bring up the color chooser. The color chooser is the wrong color, but select any any other color in the color chooser. Do CMD+Z to undo the color change. Magically the original custom color is now selected in the color chooser. Hope it helps!

@Jason Yes. You are right. We ware doing this previously :)