Two things went wrong with the operation:
1. There was resistance. Recall that Glen Doherty and Tyrone Woods were ordered to stay at the annex. They disobeyed their orders when they went to help defend the annex.
2. Stevens died...from smoke inhalation, not direct action.
Thus, the cover story involving the "Innocence of Muslims" video. While the actual gunrunning was readily defensible by referring to the Reagan administration's Iran-Contra operation, the botched kidnapping plan was the impetus for quickly fabricating a cover story.
Stevens was a casualty before the security people got there.
If this was set up by Obama, then why did Stevens have a safe room to go to?