El present perfect continuous ya tiene un verbo auxiliar, to have, y este verbo auxiliar se utiliza para la negación.

ejemplos
He has been writing a letter. He has not (haven't) been writing a letter.
She has been reading an article. She has not (haven't) been reading an article.
We have been watching TV. We have not (haven't) been watching TV.
They have been building a house. They have not (haven't) been building a house.
You have been planning a trip. You have not (haven't) been planning a trip.

En el caso de que haya un verbo modal, es este verbo modal que hay que negar. No discutimos sobre la relevancia de este tipo de construcciones. Se entiende sin problemas que construcciones de este tipo son un poco "exóticas".

ejemplos
He could not have been doing his homework.
No podía estar haciendo sus tareas
She might not have been reading an article in this moment.
A lo mejor no estaba leyendo un artículo en ese momento
They did not need to have been watching TV to get the news.
No hacía falta que estuviesen mirando la tele para estar enterados.
We should not have been partying all night instead of studying.
En vez de ir a la fiesta habría sido mejor estudiar