It doesn't matter what the track referee did in relation to the NCAA rules.
The IAAF certification form requires the referee to sign up to the following:-
"I hereby certify that all the information on this form is accurate, that the officials conducting the Competition were duly qualified and that the appropriate IAAF Competition Rules were complied with."
From the form on the IAAF's website.
Up to the referee's integrity, or (potentially) if they were watching for IAAF violations over and above NCAA violations.