Some of these characteristics have been part of the diamond since it was formed below the ground but some are a result of the cutting process and the strain it is subjct to then.

It is quite normal for diamonds to have inclusions and blemishes and diamonds without these traits are rare.
This is what makes a diamond which has few or no blemishes/ scratches much more expensive and far more valuable than other diamonds.

Diamonds are graded for clarity under 10x loupe magnification. Grades range from Internally Flawless, diamonds which are completely free of blemishes and inclusions even under 10x magnification, to Imperfect 3, diamonds which possess large, heavy blemishes and inclusions that are visible to the naked eye.

The various grades of clarity are

F-IF-Flawless or Internally Flawless. This diamond has no internal inclusions. Very rare.

VVS1-VVS2 - Very Very Slighty included. Very difficult to detect under 10x magnification.

VS1-VS2-Very Slighty included (two grades). Minute inclusions invisible to the naked eye and seen only with difficulty under 10x magnification.

SI1-SI2- Slightly Included (two grades). Minute inclusions Can be seen under 10x magnification and in some cases, in SI2, inclusions are visible to the naked eye.

I1-I2-I3-Included (three grades). Inclusions visible under 10x magnification as well as to the human eye.

The presence of blemishes, inclusions etc do lower the clarity grade of a diamond and reduce its value, they also help in identifying a diamond.

While the presence of these clarity characteristics do lower the clarity grade, and therefore the value, of a diamond they can also be viewed as proof of a diamond's identity. GIA certificates include a "plot" of a diamond's inclusions.
Diamonds are as unlike each other as snowflakes. Since no two diamonds are exactly the same, comparing the uniqueness of your diamond's clarity characteristics with the plot provided on the diamond certificate offers assurance that the diamond you pay for is the same diamond you receive.

Flawless diamonds are the rarest, and the most beautiful diamonds, a diamond does not have to be completely clean to be extremely attractive. Those diamonds with VVS and VS grades can be excellent buys as well. Most affordable are
diamonds with no inclusions visible to the naked eye. These diamonds as SI or SI2. The pricing of a diamond is also based on its clarity.