Well If you have other roots appearing in the cup I would let it just air prune themselves off over time.

If you know you have roots down lower it is not that big of a deal.

I had the same problem with a Black Weeping. Roots appearing over soil line with no other visible roots. I added soil mounted up near the roots and a week later I saw the roots exploding all over the inside of the cup.

I had no success with the baggie method, so I started mine in water and only got the white fuzzy, styrofoam looking pre-cursors to roots. Now I have roots.

Look at this way, you have the best of both worlds going- Roots AND Leaves.

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Dominick- MA