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Almost all gemstones have internal inclusions of one type or another. Non-synthetic gemstones with no flaws are extremely rare and valuable. The general degree of internal inclusion found in a gemstone also correlates to its mineralogical family. Gemstones such as tanzanite and aquamarine are generally found to have very few internal imperfections whereas emeralds and rubies are naturally found to have many inclusions. You should also realize that because each gemstone was formed under slightly different circumstances in the earth, they each bear a different set and degree of characteristic inclusions which in many cases are not considered detriments of their original beauty.