The Super Eagles were undone by two late French goals in Brasilia to signal the end of their tournament.
Midfielder Ogenyi Onazi was later spotted leaving the stadium in a wheelchair after being on the receiving end of a nasty-looking Blaise Matuidi challenge, but the American official only showed a yellow card to the Les Bleus youngster.
"I thought the referee made a lot of mistakes and was very lenient to the French players," Keshi is quoted as saying by ITV Sport. "There was a very bad tackle on Ogenyi Onazi and he is probably out for weeks."
France will face either Germany or Algeria in the quarter-finals.