Final answer:
President Lincoln's suspension of Habeas Corpus, allowing the detention of suspected Confederate sympathizers without formal charges, was seen as a controversial limitation of civil liberties.
Step-by-step explanation:
The decision by President Abraham Lincoln that was controversial because it involved limiting people's civil liberties was the suspension of Habeas Corpus. During the Civil War, Lincoln suspended the writ of habeas corpus to allow authorities to arrest and detain suspected Confederate sympathizers without a court hearing or formal charges. This move was highly controversial as it limited an essential liberty protected under the Constitution. The suspension was seen as a necessary measure by Lincoln and his administration to preserve the Union during a period of rebellion and warfare, but critics viewed it as an overstep of presidential authority and an assault on individual rights.