It is fair to say that several exchanges - most notably Gox of course - were tracking transactions in a way that was inherently unsafe. That, in combination with poor communication about a complex situation to the market, is what resulted in the losses.
I am aware of the distinction. However from a consumer point of view it matters not whether the fault lies in the protocol or the wallet implementation. The consumer lost their investment due to exchange insolvency due to something happening which should not have happened. That's a bug.