I need examples of coordination failures (2 or 3) between Humanitarian
organizations e.g. NGOs during complex emergencies like Somalia, Haiti
or Afgahnistan. I am looking for factual news stories or articles that
detail events where a lack of coordination or communication between
NGOs resulted in a loss of relief aid (like food or medicine spoilage)
or loss of life.

This study isn't exactly what you're looking for, but it might relate
to your studies.  It focuses on how humanitarian efforts have
sometimes exacerbated conflict.

Humanitarian Action: The Conflict Connection
http://www.brown.edu/Departments/Watson_Institute/Publications/OP/op43.pdf

This occured in October 2001. (twice)

"Pentagon sources told CNN Monday that the military's probe also found
numerous clerical errors, which led to the mistaken bombings,
including the failure of the Red Cross to notify the United States it
was using the warehouse complex to store wheat and other humanitarian
supplies."
March 19, 2002 Posted: 2:18 AM EST (0718 GMT)
From Jamie McIntyre
CNN Military Affairs Correspondent
http://www.cnn.com/2002/US/03/19/ret.pentagon.redcross/

://www.google.com/search?hl=en&ie=ISO-8859-1&q=red+cross+warehouse+bombed

Thank you both (very much) for your comments. I need one or two more
just like the bombing incident. I recall CNN or MSN running a story of
food spoiling in an Afgahn warehouse because various NGOs didn't know
it was there. For the life of me, I can't find anything on it.

This is probably not a example you are looking for.  It showed a
problem of coordination within our government.

"At least one person has been killed and others maimed after mistaking
unexploded cluster bombs for the food packets, which are the same
bright yellow colour."
http://news.bbc.co.uk/1/hi/world/south_asia/1670891.stm

://www.google.com/search?hl=en&ie=ISO-8859-1&q=bomblets+food+packets

This might be a good starting point to find the actual stories.  I
think most of their information came from Turkish newspapers.

MIDDLE EAST TECHNICAL UNIVERSITY 
INDUSTRIAL ENGINEERING DEPARTMENT 
IE 404 MANAGEMENT FOR ENGINEERS
DISASTER MANAGEMENT FINAL REPORT
"In this project, the main aim was to examine the three most important
institutions, which are relevant to the Disaster Management, namely
Red Crescent, Civil Defense and Disaster Affairs, and comment on the
weaknesses of these institutions observed during the rescue operations
from the management point of view."
http://www.geocities.com/asterix_metu/HAMITGUNASAN.html