Why was the constitutionality of President Lincoln's suspension of habeas corpus brought into question?

Due to imprisonment of citizens without a trial.

Explanation:

April 27, 1861 President Lincoln issued an order which proclaimed that the writ of Habeas Corpus will be suspended on grounds of public safety because of the ongoing Civil War. President Lincoln vetoed this order and also imposed Martial Law all over the country.

The constitutionality of Lincoln's order was questioned when secessionist John Merryman was arrested and denied from being released under the Habeas Corpus writ. In support of Merryman's appeal, Chief Justice Roger B. Taney also questioned Lincoln's authority to deny the citizens the right to the writ of Habeas Corpus.

In a nutshell, it can be understood that President Lincoln used his authority decisively without taking Congressional consideration on the issue of Habeas Corpus.