Only nine hurdles had been set out instead of the regulation 10 at the Great City Games in Manchester, northern England on Sunday.
Ennis described it as a "massive, massive mess-up."
The Briton had clocked 12.75 seconds into a headwind to beat Olympic champion Dawn Harper and world silver medallist Danielle Carruthers.
In a statement organizers said: "We would like to apologize for this unacceptable incident."
They blamed UK Athletics, who are employed "to manage this vital element of the event on our behalf, and we will of course be investigating this unfortunate occurrence with them."