The heptathlete clocked 12.75 sec, 0.04sec faster than her previous best, but it emerged after the race at the City Games in Manchester that only nine hurdles had been set out rather than the regulation 10.
“I am so annoyed. I still had a good competitive race, but I’ve just not got the result I wanted,” said Ennis.
“It’s a great event but that’s a massive, massive mess-up.”
A tournament spokesman said: “There has been a technical error and there were nine sets of hurdles out on the course instead of 10.
“We’ll conduct a thorough investigation and find out what happened and why and by whom.”