I see two possibilities: 1) the flight plan was known to the officer in charge of the SAM site and he was under orders to shoot the plane down and now they’re trying to cover it up or 2) it was a genuine mistake and so there was some kind of miscommunication or perhaps the air defence forces weren’t even looking at flight plans and just shooting at anything that looked suspicious on radar. Gross incompetence and lack of training and coordination in the Russian military are all issues we’ve come to expect so it’s easy to see how this could happen without knowing for sure. And since Russia seems to be in full denial/obstruction mode we might never know exactly what went wrong.