It happens all the time in our world, too, judging by witness statements - stuff vanishing in thin air, people spontaneously combusting or giving birth to three-headed Elvises. Those reports didn't grow scarcer during the paranoia of, say, 1960s United States, but didn't exactly ignite WWIII, either.
So a box glimmers and ceases to be? Not even a Vulcan could think such a thing would have consequences.
But we have plenty of precedent to handheld communicators being unbeamable unless somebody is properly operating them. Kirk kept losing his; he never suggested beaming it to safety, sometimes for obvious story reasons, but sometimes not. And nothing much got beamed unless it had an active communicator on top of it.
Timo Saloniemi