This article from the WSJ lays the blame for the logistical mess on the local office of emergency management, which it refers to as the local FEMA. See: FEMA’s Foul-Up in Puerto Rico. “The emergency plan depended on generators but diesel was not delivered.”
Apparently the author is referring to either the The Municipal Emergency and Disaster Management Office, which includes San Juan, or the Puerto Rico State Agency for Emergency and Disaster Management. I cannot tell which from the article.
Update: I just read over some of the nearly 450 comments on the above article, and it is clear most of those responding do not understand our federal system and that there are 3 tiers of emergency management. It remains unclear to me where the author of this article is pointing blame.