Authorities suspect he went on to kill Tom Clements, who led the state's prison system, last month. They have also said there is a "strong connection" between that killing and the murder of Nathan Leon, a pizza delivery driver who was found dead in suburban Golden, Colorado.
"The district has undertaken a review of its practices in an effort to avoid a reoccurrence of this circumstance," Charles Barton, chief judge of the 11th Judicial District, and Walter Blair, district administrator, said in a Monday statement.
"The court regrets this oversight and extends condolences to the families of Mr. Nathan Leon and Mr. Tom Clements."
Ebel went to prison in 2005. He was serving an eight-year sentence when he assaulted a prison guard.
He entered into a written plea agreement, which stated Ebel would plead guilty to assault in the second degree and that the court would impose a consecutive sentence of up to four years plus a mandatory three years of parole.
A sentencing hearing was held in June 2008.
"The judge announced a sentence of four years in the Department of Corrections but did not state it was consecutive because it was already required by the terms of the plea agreement," read Barton's and Blair's statement.
"Because the judge did not expressly state that the sentence was consecutive, the court judicial assistant did not include that term in the mittimus, the sentence order that went to the Department of Corrections."
Noted Denver-area attorney Scott Robinson represented Ebel in four cases from 2003 to 2005. They lost contact after that.
"If you were writing fiction, you might have trouble understanding this thing to be true. Catastrophic for three families -- the Clements, Leon and Ebel families," he said.
"What's really agonizing about this situation is it was an utterly routine plea bargain. A mundane task a judge undertakes every single day. Here we are five years later looking at the wreckage that was the result of those errors."
Clements was shot to death at his home outside Colorado Springs on March 19. Ebel was killed two days later in northern Texas in a gun battle with authorities that left a sheriff's deputy wounded.
CNN's Mark Morgenstein contributed to this report.