YES, they did. TWICE. Ex Parte Merryman in 1861, and Ex Parte Milligan in 1866.
...and Copngress specifically suppported the President's action. Remember, Congress was out of session...
When did the Legislative Branch suspend the writ as the Constitution clearly shows only they can?
Morever, the Founding Fathers' Milita Act 0f 1792 authorized the President to put down rebellion without congressional authorization, and rounding up rebels and throwing them in prison is part of putting down rebellions.
He could arrest and charge "rebels" with a crime, couldn't he? But he didn't, did he? He chose instead to violate the Constitution and throw out the Bill of Rights in order to deal with his "problems" using police state tactics against his own citizenry in the North. His suspension of the writ of habeas corpus was illegal, and a blatant violation of the Constitution.
Would you please cite the Act of Congress to which you refer and the date it was approved.