The negative selection in the thymus may not be fully functional to eliminate self reactive cells.
Not all self antigens may be represented in the thymus or certain antigens may not be properly processed and presented. Hence, to some extent autoimmunity is present in everyone and facilitates autoimmune pathology in some individuals, but in others they are components of protective mechanism.
The escape of auto reactive cones allows immune system to mount an effective and specific immune response against self determinants.