China has said US navy ships were not turned away from Hong Kong because of a misunderstanding, but because the US had "harmed" relations with China.
The fleet was to stop in Hong Kong for a Thanksgiving holiday visit
A Chinese foreign ministry spokesman said US arms sales to Taiwan and Washington's award of a medal to the Dalai Lama had damaged relations.
The White House earlier said China's foreign minister insisted the incident was a misunderstanding.
The US says it is seeking clarification on why the ships were turned away.
The ships, including the aircraft carrier Kitty Hawk and eight support vessels, had been due to stop in Hong Kong for a long-planned visit timed to coincide with the US Thanksgiving holiday on 22 November.
Hundreds of family members had flown from the ships' base in Japan to greet the 8,000 sailors in the fleet.
The ships were refused access to Hong Kong's harbour and spent most of the weekend on the South China Sea before returning to their base in Japan.
China then reversed the decision, citing "humanitarian reasons".
A White House official on Wednesday said Chinese Foreign Minister Yang Jiechi told Mr Bush the ships were turned away because of a misunderstanding.
But on Thursday, Chinese foreign ministry spokesman Liu Jianchao said: "Reports that Foreign Minister Yang said in the United States that it was a misunderstanding do not accord with the facts."
He said Sino-US ties were developing well but "bilateral relations have been interfered with and damaged by mistaken actions by the US.
"For example, US leaders have met with the [Tibetan spiritual leader] Dalai Lama."
And, he added, "we have grave concerns with US arms sales to Taiwan".
White House spokeswoman Dana Perino said on Thursday that the US authorities were seeking clarification of the Chinese moves.
She said "it was wrong for this ship to be turned away. It inconvenienced an awful lot of families who had plans to be there to spend Thanksgiving with sailors who are on that ship."
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.