If you are talking about seeing a red square when you place a sample, that is an indication that the brightness level in the sample exceeds the Tolerance value in Model Parameters (1).
Personally, I always crank the Tolerance to 5 or 10. I then use extra care to ensure that my samples are placed only over background sky. I never place samples over any stars or any nebulosity or other object.
Yeah... it is also possible the shadows relaxation could come into play... but if the variations are that large in the image- the non-uniformities are likely "challenging." But as Wade said, increasing the tolerance is a good first step.
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