The jury is not expected to return to court until Monday. The court did not make clear what the issue was and it was discussed in chambers.
But so far, the panel has already lost two alternates.
The judge ordered a group of 19 jurors to sit through what is expected to be a two month trial that will determine whether Arias should be condemned to death for the 2008 murder of her boyfriend Travis Alexander. Arias, 34, was convicted last year of killing Alexander with a gunshot, 27 stab wounds and by slitting his throat. But the jury was split on whether Arias should be executed, requiring a second jury for the sentencing phase of the trial.
The plan to have seven alternate jurors for the sentencing phase was whittled to six on the first day when one juror didn't showed up because of a family emergency.
If a third juror gets booted, the trial will be left with four alternates as the lengthy trial is just beginning.
The trial promises to be an ordeal with lots grisly testimony and photos about the wounds, as well as raunchy photos, texts and phone message between Arias and Alexander. On the first day of the trial prosecutor Juan Martinez showed the jury a photo of Alexander's gaping neck wound.