The kernels inside of nectarine pits do contain a small amount of cyanogenic glycosides, which the body metabolizes into cyanide. However, the amount is so small that one pit is of little threat to an adult.
Many fruit pits commonly contain a small amount of cyanogenic glycosides, and nectarines are no exception. However, the very small amount present is unlikely to cause harm to an adult due to accidental ingestion. In fact, small amounts of these kernels are sometimes used as an aromatic to enhance other foods. More caution should be taken with children and pets, as they have a lower resistance to toxicity, though the bitter flavor makes purposeful ingestion less likely.