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It is not unusual to have some negative values in some pixels of every band. It just means that FLAASH was unable to create an appropriate model for those pixels. They are often areas of very low (or sometimes very high) radiance. You can try and reduce this effect by increasing the visibility amount to 80-100km if the scene is very clear. While this may increase your scaled reflectance to 0 or some small amount, it is still likely to be a very insignificant reflectance value when considering the output is scaled by 10,000. For exaple, if it now returns a value of 10, the percent reflectance is 10/10000 = 0.01 % reflectance.
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