While being flawless is highly desirable in a diamond, sometimes the inclusions in a coloured stone can be a good thing; they share information about the origin and nature of the stone, and allow us to easily confirm that the stone is not a synthetic.
The image below is a magnification of a 7.89 carat sapphire. When we look inside the white box, we can see some faint inclusions, in straight lines, at an angle of 70 degrees to each other. In the second photo, the inclusions, called “silk”, are marked out with red lines (they are in a slightly different plane to the photo, so the angles seem to be less than 70 degrees in the photo)
These inclusions, along with some other evidence, allowed this stone to be identified as natural, unheated sapphire, from Sri Lanka. (Most sapphires are heated to enhance the colour. This is normal, permanent, and detectable. The heating changes the structure of some inclusions, and can be seen under a microscope. It is rare to get a sapphire of good enough colour to not need enhancement).
The inclusions can also give us information about where the sapphire came from: taking the example below the distinctive mixture of microscopic inclusions is very revealing:
In the upper left and bottom right we can see a pattern of small, short lines. These are called rutile needles. In between, in the centre of the photo, running diagonally from top left to bottom right, are parallel, unbroken lines. This is called silk.
The unbroken pattern of silk tells us that the sapphire is of natural, unheated colour. The fact that there is silk and rutile needles in close proximity indicate that the sapphire is most likely from Sri Lanka. (Other, inclusions, not photographed here, called lixiviated fluid drops, confirmed the identification.)