I'm just curious.

Zero Five's treatment went on for far longer than expected, which forced Zero Three to leave for her duties. 

With just Nine accompanying her, the two were ordered to not move too far from the base. 

Two Valkyries weren't by any means weak, but after the incidents from the day before it would be too reckless to let them do the usual.

Time passed and the Valkyries returned. Zero Five was still in the pod, leading to Zero Three getting depressed once more. She asked why it was taking so long, and why Eir was incapable of determining the amount of time it would take for the treatment to be completed.

Sam explained that the device provides a rough estimate of how long it will take however some things happen on the microscopic level that might result in that estimate being extended. The damaged parts are basically being 3D printed using nano machines, but due to the complexity of the Valkyries' bodies, some mistakes are bound to happen.