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 that 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






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