Gemstones contain a wide variety of "inclusions." In a faceted gem, an inclusion is defined as anything that will interfere with the free passage of light. They can be little bits of minerals, hollow areas, or fractures.
As with color, tiny differences, which are only apparent to the grader, have a significant effect on value. The best examples of this are diamonds. There are several grades where the inclusions are invisible to the naked eye and have no affect on the beauty of the stone. Yet the difference in value, between something that is very difficult for an expert to find with 10-power magnification and something that is easy to find with magnification, is substantial.
Most colored stones are simply graded "eye clean," (meaning that the inclusions are not visible to the naked eye,) slightly, moderately, or heavily included. Gems with eye visible inclusions are always lower in value, but the change is not applied equally. There are three classes of colored stones, those that are "usually clean," those that are "usually included," and those that are "almost always included." Emeralds fall into the last category. Their clarity cannot be compared with other gems. If you want an emerald without any eye visible inclusions, you are limited to small stones. If you want a larger emerald, you will have to accept a certain amount of inclusions and find its value in the color. Fractures and cracks are not allowed in astrological gems.