The US has formally protested to China over its refusal to allow a number of US ships to dock in Hong Kong.
The fleet returned to its Japan base without stopping in Hong Kong
The ships had been scheduled to dock for Thanksgiving, and hundreds of family members had flown out to greet the 8,000 sailors on board.
The White House says President Bush also raised the issue with the Chinese foreign minister.
China insists the incident was a misunderstanding, but US Navy officials have demanded a full explanation.
The US fleet, which included the aircraft carrier USS Kitty Hawk, spent most of Thanksgiving weekend on the South China Sea after being refused permission to enter Hong Kong harbour.
China eventually reversed the decision for "humanitarian reasons only", but by then the ships were already making the return journey to their Japan base.
A White House official said Chinese Foreign Minister Yang Jiechi told Mr Bush the ships were turned away because of a misunderstanding.
The official did not say what the misunderstanding was.
'Perplexing and irritating'
Speaking on Wednesday, Pentagon spokesman Geoff Morrell said the US would be officially expressing "displeasure" to the Chinese military attache in Washington.
"It's regrettable, and we have not received to date sufficient explanation as to why it took place.
"I think that's why this incident is so baffling to us, because there is no indication at all prior to the Kitty Hawk being refused entry to the port of Hong Kong that there was any reason or any cause for concern."
The USS Patriot and the USS Guardian eventually refuelled at sea and returned safely to Japan.
Senior US Navy officials have also expressed concern that China recently refused permission for two US minesweepers to take refuge and refuel in Hong Kong during a tropical storm.
They said the refusal was "perplexing" and "irritating".
"It is not, in our view, conduct that is indicative of a country who understands its obligations as a responsible nation," Pacific commander Admiral Tim Keating told reporters.
But he added that the incident was not "calamitous" and that he hoped it was not the start of a continuing blockage on port visits.