Using a weapons system without fully understanding how to operate it. If you mean it was a "mistake" as in the operator failed to identify the thing he was intentionally firing at, then yes- it was probably an accident. A case of mistaken identity. But as the saying goes, intent follows the bullet. Yes, the plane was intentionally shot down. Just not what they were expecting.
And the black boxes are utterly irrelevant. All of the radar and surveillance data conclusively shows it was a missile and most likely, based on the audio recordings released, fired by the Russian insurgency. Testing of soot and scoring on the exterior of the airframe should evidence exactly who is responsible.
