Hybrids are the offspring of Hollow Child mothers and human fathers. Unlike their mothers, they are completely organic.
They are discovered by the Rust Crew during their search of Amada's headquarters. According to the Amada AI, they have perfect mental and physical health from the moment they are born. Amada's records indicate that 108 hybrids exist in the world, among them being Rust Crew member, Faye Lee.
Despite their completely organic nature, and lack of hostilities, they are seen as a threat by members of the IRTA, based on the fact that they were not born from a human mother. Due to this irational xenophobia, they only see the hybrids as a threat, more "dangerous" than the Hollow Children who gave birth to them.
When Charlie relays the existence of the hybrids back to Geneva, they order Rust Crews be sent to eliminate them. The joint chiefs state (rather hypocritically) that the world has enough racism.
After the events of Binary Domain, the IRTA know the locations of all hybrids except Faye, who has gone into hiding to protect herself. They only see her as a threat, in spite of her long service.