The constitutionality of the internment was a large issue. Arresting American citizens and putting them in camps is against the law and the constitution in many instances. 
 "You may think that the Constitution is your security — it is nothing but a piece of paper. You may think that the statutes are your security — they are nothing but words in a book. You may think that elaborate mechanism of government is your security — it is nothing at all, unless you have sound and uncorrupted public opinion to give life to your Constitution, to give vitality to your statutes, to make efficient your government machinery." - Charles Evan Hughes, Chief Justice, U.S. Supreme Court

Broken Amendments 

The 6th amendment states "the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the State and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor, and to have the Assistance of Counsel for his defense." 
Japanese people were taken into the internment camps. None of them had a fair trial, and if they refused to cooperate they were sent into prison. 

The 11th amendment states "The enumeration in the Constitution, of certain rights, shall not be construed to deny or disparage others retained by the people." 

The United States government took away over 110,000 innocent Japanese-American rights by throwing them in prison for no reason.

The 14th amendment states "No State shall make or enforce any law which shall abridge the privileges or immunities of citizens of the United States; nor shall any State deprive any person of life, liberty, or property, without due process of law; nor deny to any person within its jurisdiction the equal protection of the laws."

Executive order 9066 was essentially a law that took away the liberties of some 110,000 United States citizens without due process of law.