I would imagine the issue is the Tortle's features for their unarmed is competing with the Monk's feature, and the Tortle is winning. I'm not familiar enough (yet) with how the scripting works to come up with a solution off the top of my head. You may want to look into using an adjustment for now to override the damage dice of the unarmed attack to match up with the martial arts dice. It's manual, but it's better than nothing.
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