The friendly fire incident happened on Sunday at the Hendijan-class support ship Konarak near the port of Jask on the Gulf of Oman.
US President Donald Trump had initially said no Americans were hurt by the missiles fired on a base housing US soldiers in the country's west on January 8.
Pentagon spokesman said that of the 50, 31 were treated in Iraq and returned to duty while 18 were being evaluated in Germany.
His comments came hours after Iran launched missile strikes against two US military bases in Iraq in retaliation for the killing of its top commander General Qassem Soleimani.
Shortly after midnight on Wednesday, Iran fired a series of missiles at bases in Iraq housing US troops, officials in Washington and Tehran said.