The judge in the Atlanta Public Schools cheating trial declined to throw out two of the 27 counts against one defendant because of mistakes, but he said the jury should still strictly consider what is written in the indictment.

It’s the first significant wrench to come up in deliberations in the racketeering case against 12 defendants — former school administrators, principals and teachers — who are accused of conspiring to change answers on a 2009 standardized test to inflate scores.

On Thursday afternoon, the jurors asked what they should do about problems they saw in two of the charges against former regional director Sharon Davis-Williams. The school named in count No. 5 should have been listed in count No. 6, and the school named in count No. 6 belonged in count No. 5.

Davis-Williams’ lawyer, Teresa Mann, questioned the mistake in a motion filed more than a year ago, then again last month in her motion for a directed verdict of acquittal, and yet again in her closing argument to the jury on Wednesday.

Prosecutors had assured Fulton County Superior Court Judge Jerry Baxter last month that the indictment was accurate. On Thursday they described the mistake as a “scrivener’s error.”

The judge was visibly angry.

“I was misled,” Baxter shouted.

The jury of six men and six women were called into the courtroom and told to “strictly” follow the indictment.

The question was raised after the jurors had deliberated just over two hours.

One of the questioned counts says Davis-Williams committed the crime of making false statements and writings when she covered up a report by a school proctor that students at Perkerson Elementary School said a teacher helped them with answers on the 2009 Criterion-Referenced Competency Test. The indictment should have said it happened at Herndon Elementary School.

In the other count questioned, the indictment said Davis-Williams told a classroom monitor to change his written report that he saw a teacher at Herndon Elementary help students during the 2009 CRCT. In that instance, it should have noted the alleged crime happened at Perkerson.

“This isn’t a scrivener’s error,” Mann said. “A scrivener’s error is a mistake in a name. This is how they presented it to the grand jury.”

Davis-Williams remains charged with one count of racketeering and two counts of making false statements or writings. Last week, Baxter dropped a count of false swearing against Davis-Williams.

After months of testimony, the jury began its review of the conspiracy case against 12 former educators Thursday morning. They will take off Friday and return to their discussions on Monday.

It could be days or weeks before the dozen defendants know if they will be allowed to return to their lives or go to prison.

The jury was dispatched to the deliberation room at 10:10 a.m. Thursday, moments after the judge completed a 55-minute explanation of the law. The seven alternate jurors stayed behind so Baxter could explain their status and to thank them.

Baxter told the alternates they could leave but could be called to fill in if something happens to one of the 12 jurors. One of the alternates asked if they could say goodbye to those left behind.

Baxter said they could go hug each other, “but don’t make it last all afternoon.”

Laughter and cries greeted the alternates when the deputy opened the door to the jury room.

The 12 jurors have with them thousands of pages of evidence, their notes and memories of almost five months of testimony and three days of closing arguments.

All involved in the case expect it to take the jury days, if not weeks, to reach a decision. Baxter told attorneys in the case they can leave the courthouse, but they should be nearby if the jury has questions.

One of the defendants, Shani Robinson, was excused from waiting at the courthouse for the jury to reach a verdict. Robinson is due to give birth to a son in mid-April.

The former educators are accused of conspiring to change answers on the 2009 CRCT to artificially inflate scores to satisfy federal benchmarks. The prosecution said bonuses and raises were awarded based on test scores.

The alleged cheating was discovered when The Atlanta Journal-Constitution reported inexplicable spikes in test scores. Eventually, a criminal investigation was opened which led to a 29-count indictment two years ago. Two of those counts have been dropped, leaving 27 for the jury to consider.

According to the charges, former Superintendent Beverly Hall was the ringleader. She was not tried because she was being treated for breast cancer when jury selection began. Hall died earlier this month after testimony ended. One other former educator named in the March 2013 indictment also died. Twenty-one others pleaded guilty to lesser charges and were sentenced to probation.

A racketeering indictment could mean a 20-year prison sentence. The other felonies carry prison sentences of as much as five and 10 years each.