MySQL NOT IN consulta no funciona

¿Hay valores NULL en taxon_name_element.parent_id? ?

La consulta...

select taxon_id 
from taxon_name_element
where taxon_id not in (
    select parent_id
    from taxon_name_element
)

...es equivalente a...

select taxon_id 
from taxon_name_element
where
    taxon_id <> parent_id_1
    AND taxon_id <> parent_id_2
    ...
    AND taxon_id <> parent_id_N

...donde parent_id_X son valores reales que están actualmente en el parent_id columna. Si incluso uno de ellos es NULL, el correspondiente taxon_id <> parent_id_X las expresiones se "colapsarán" en NULL, arrastrando toda la expresión WHERE con ella.

Filtre los valores NULL para obtener lo que desea:

select taxon_id 
from taxon_name_element
where taxon_id not in (
    select parent_id
    from taxon_name_element
    where parent_id is not null
)