It sounds like you found some unexpected items in your sugar cookies after baking. To better understand what these might be, could you describe their appearance? Often, things like undissolved sugar or unevenly mixed ingredients can show up unexpectedly. If the spots are just sugar or harmless ingredients, the cookies should be safe to eat. However, if you're unsure about what these spots are, it might be best to discard this batch to be on the safe side.
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