The three-minute ad, which features stars such as Wayne Rooney, Didier Drogba and Cristiano Ronaldo, ended 10 seconds early - before the Nike logo could be displayed.
ITV are due to receive the bumper payment from the sportswear manufacturer for the primetime slot immediately after the final whistle - but may now have to write it off.
"It is disappointing," said a Nike spokeswoman. "We're waiting to hear back from ITV."
ITV spokesman James Macleod said: "We are looking into the cause of the issue and are in close dialogue with Nike about it."
The 'Write the Future' ad was screened simultaneously in 32 countries.
Directed by Mexican star Alejandro Inarritu, it features Rooney being knighted by the Queen for a match-saving tackle - having contemplated living out his life as a loner had he not made it - Ronaldo nutmegging Homer Simpson and NBA legend Kobe Bryant performing a Ronaldinho-esqe scissors move to celebrate a basket.
- Cristiano Ronaldo
- Wayne Rooney
- Didier Drogba