Why are there holes in the atmosphere?

The hole in the ozone layer, if this is what you are referring to, is an annual event that occurs after the long night period of the Antarctic winter. It is due, primarily from a lack of sunlight causing ozone to be continuously made.

Ozone is a very unstable gas and must consistently be absorbing the sun's incoming radiation in order to exist. When the winter months start and the sun disappears for the next few months, the ozone layer starts to decay. When the sun returns, the hole disappears within a few weeks.

A smaller, but similar event occurs over the Arctic during it's winter period.

It is believed that CFC's that are produced for refrigeration are adding to this issue.