For all practical purposes, ALL emeralds have inclusions in them. An inclusion is anything included in the crystal, which if flawless would be perfectly clear. The inclusions may be foreign substances such as iron pyrite crystals, or water trapped in the crystal structure as it formed; but the most common inclusions are actually gas (air) veils and bubbles that were trapped during formation. These may run the gamut of the slightest spots or veils at one end of the spectrum, to those making the stone opaque at the other.
You will often hear reference to stones being eye-clean. What this would normally mean is that the stone has no inclusions visible to the naked eye. A more stringent standard would be loupe-clean, which would be a stone without inclusion detectable with a 10-power jeweler's loupe (magnifying glass). This latter case would be remarkable clarity in the case of an emerald. (see Using a Loupe)
Diamonds that you would normally buy are differentiated in grade (and price) by tiny differences in the number and size of imperfections visible only with a jeweler's loupe, whereas in the case of emeralds you will most likely be able to see inclusions with your naked eye. Because of this characteristic, emerald salespeople may try to put a positive spin on things. They might say that these inclusions are gardens (or in French, jardins), and may even suggest that such inclusions prove that the emeralds are natural, or in other ways are a positive attribute. Having a garden in your stone sounds much nicer that having a flaw, does it not? But this is misleading. The fact that we must accept emeralds with visible inclusions does not make these imperfections a virtue.
In the interests of hiding or minimizing these blemishes, numerous techniques have been developed to accomplish what is known as clarity enhancement. (see more) The most important thing for you as a buyer is to be able to have complete confidence that you are being told the truth about any and all treatments or enhancements present in the stone you are considering.