SDEROT, Israel — It was 1:30 p.m. on Friday in Sderot, and Ido Avigal, 5, was being laid to rest a few miles to the north. He had been killed in what officials termed a freak incident two days earlier when a rocket from Gaza made a direct hit on the building next door to his aunt’s apartment, where he was visiting with his mother and older sister.

When that rocket struck on Wednesday evening, he was sheltering in a fortified safe room meant to protect residents from this exact threat. But a piece of shrapnel managed to puncture the thick, steel shutter and the thick glass window of the shelter, mortally wounding the boy. Ido’s mother and his sister were also injured while inside the room.

It was the first such case of a death in a fortified safe room that military officials could recall.

“So should we not trust the safe room now?” asked Andrei Mardachayev, 38, who lives in a building about 250 yards away and had come to view the damage with his wife, Irit, and their three young children.

“No, no, don’t say that,” Ms. Mardachayev said, aware that the children were listening. “We still have to go in it when the siren goes off.”