Final answer:
Abraham Lincoln's controversial action that limited the rights of certain U.S. citizens during the Civil War was the suspension of habeas corpus, allowing for the detention of individuals suspected of Confederate sympathies without trial.
Step-by-step explanation:
The controversial action that Abraham Lincoln took early in the Civil War, which limited the rights of certain U.S. citizens, was the suspension of habeas corpus. This action, taken in an effort to quell secessionist and pro-Confederate activities, allowed for the arrest and detention without trial of those suspected of supporting the Confederacy. Lincoln's move was seen by some as necessary for preserving the Union but criticized by others as an overreach of executive power. Notably, this suspension included the Habeas Corpus Suspension Act passed in March 1863, which expanded this power.
Although the Emancipation Proclamation was also a significant and controversial action, it was not the action that limited the rights of certain citizens. Instead, it declared the freedom of slaves in the Confederate states, but did not apply to Union states or Confederate areas under Union control. The Emancipation Proclamation was primarily a military measure to weaken the Confederacy's war effort.