Issue when doing Levels as last step

After using the Healing Brush, Clone Tool, Sponge tool, etc. I do Levels Adjustment Layer and it results in the issues in the attached image. Is there a way to avoid this other then doing Levels at the very beginning? The only other way I found around this was to flatten the image prior to doing Levels.
Thanks.

I would guess from the image you posted that you cloned and healed onto a new empty layer and when you added the level adjustment layer you clipped it to that layer when it should be applied to all layers not just the clone and healing layer.

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    Hi,
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