(CNN) Late Thursday night as briefs and orders ricocheted through the clerk's office, the Supreme Court struggled again, at the last minute, with the death penalty.

Two times an execution was temporarily delayed by Justice Clarence Thomas in order to give the justices more time to consider the case. Ultimately, the execution of Alabama inmate Ronald Smith, was allowed to go forward—by a deadlocked court.

Chief Justice John Roberts, who in November sided with liberal justices as a courtesy to stay the execution in a similar Alabama death row case, gave no such temporary reprieve to Smith, who was convicted of killing convenience store worker Casey Wilson in 1994. While it takes only 4 justices to agree to hear a case, it takes 5 to block an execution.

The last-minute legal drama that unfolded will remain shrouded from public view; a justice's vote in a motion for stay of execution is rarely explained.

Unlike most Supreme Court cases, which are the subject of public arguments and lengthy opinions, last-minute deliberations on death row cases are usually opaque. One law professor calls it the court's "shadow docket."

When Chief Justice John Roberts provided the so called "courtesy vote" last month he did something rare: he explained why.

"I do not believe that this application meets our ordinary criteria for a stay," Roberts wrote, before saying he would vote to delay as a courtesy and to give his four liberal colleagues more time to review the case.

The same four colleagues wanted to delay Smith's execution, but Roberts issued no explanation on why he didn't think the case warranted his courtesy vote .

Smith's case highlights at least two brewing divisions on the court that won't be publicly aired in the coming days, especially since Smith was put to death at around 11 pm.

First there is the issue of why Roberts didn't supply a courtesy vote this time around. That lack of transparency raised more questions than it answered late Thursday night.

"In these shadow docket cases, the Justices don't write opinions," said William Baude of the University of Chicago Law School. "They usually don't write anything—they just vote and move on." Baude has written extensively on the issue in the NYU Journal of Law & Liberty noting that some of the court's orders "lack the transparency that we have come to appreciate in its merits cases." In the merits cases, which have justices have agreed to hear publicly, the court shows its work, dedicating pages to majority opinions and dissents. That doesn't often happen when the court is faced with an emergency application, such as a stay of execution.

"While the Court follows regular processes to produce public and reasoned opinions, its internal deliberations are afforded far more secrecy than the other two branches" Baude wrote.

Roberts most likely has very good reasons for choosing not to grant the courtesy vote, but they won't be revealed publicly.

The second is whether a judge can overrule a jury's recommendation of life without parole, as happened with Smith.

The Supreme Court struck down a similar sentencing procedure in a case out of Florida called Hurst v. Florida.

Alabama's Attorney General, Luther Strange argued that Smith's petition presented "an unusually large number of procedural problems" and he noted that Hurst has "no retroactive application to Smith."

One more issue involved in the case became relevant during the execution when witnesses say that Smith appeared to be struggling. According to local reports Smith—who had also challenged Alabama's lethal injection protocol-- coughed and heaved for about 13 minutes.

Alabama's protocol includes a drug called midazolam that has been linked -- in different doses -- to botched executions in other cases.

Controversy over the drugs used to kill death row inmates is not new. "Once again a state conducted an execution that was a failed experiment," said Dale Baich an Assistant Federal Public Defender in Arizona, who represents prisoners in lethal injection challenges. "As long as states continue to use midazolam as part of the lethal injection process, there will be more botched executions," he said noting that the issue is being litigated in Ohio.

Steve Vladeck, CNN contributor and professor at the University of Texas School of Law, says the unanswered questions provide less clarity to the litigants, the lower courts and the public. "It complicates any effort to divine some deeper lesson from the Court's decision—including whether it agrees with one side on the merits; whether some procedural obstacle prevented it from even reaching the merits; and so on."

"The problem is only exacerbated when the Court splits 4-4 , because although we at least know the vote, we have even less insight into the underlying reasoning," he said.