Answer: As long as you do not allow debris to collect in the area, the water should drain on its own. I wouldn't recommend filling the crotch with anything because the bark and branches will continue to grow. Any foreign matter can trap excess moisture and inhibit natural growth of the bark. Just make sure leaves, etc. do not collect in the area. As the tree grows, the crotch will become smaller and less apt to collect rainwater.
Best wishes with your landscape!
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