I think it's just data storage incompetence; this isn't the only time this has happened, and it hasn't only happened in this "direction," too. I mean, Clinton loves playing dirty, but this would too easily blow up in her face. Now, the DNC is all in line for her, so I could see people pushing for her basically taking advantage of the situation try and gut shot Sanders' campaign, but ultimately I don't think it's likely at all that this whole thing was a staged move to take him down because it would simply be overplaying their hands; as it stood they could have just let it play out diplomatically and she ultimately gets the nod with his endorsement. Now there's a serious chance of that not happening because of acrimony.
I think, however, Sanders lashing out like he did was unexpected. Look at it this way: this is the kind of thing Clinton and co. could play magnanimous about and like the damage be done by the moderators grilling Bernie about it at the debate. Him making a stink doesn't work in her favor it at all; it only serves to make him a legitimate threat for the first time. He can raise enough of a stink to piss off enough of his supporters enough to kick in the liberal instinct to not vote for anyone since he was done wrong, or, worst-case scenario, this pushes him to make an independent run.