It happens to me frequently, it's almost reproduceable if I'm alt-tabbed out when the interdiction begins and I have to activate the game window again. No matter how fast I slam the throttle to zero and submit, their side of the mini-game bar flies up to full red and I get FSD failure and take damage.
I've had it happen to me a couple of times in the past few weeks, but always when the target has shot out of view. It takes a second or two for the submission to 'kick in', and if you don't stay pointing somewhere in the vicinity of the target crosshairs, you can lose the interdiction in that period and end up with damage. Could that be the case here?
I had so many different outcome to interdiction i totally think the damage model/mechanics is random - I wish FD would provide official statement as so far i only got players feedback.
For example i had few times where i submitted - hull shows 100% and yet when i dock i have both repair and wear&tear price to pay - in a Conda this is not cheap !! (and yes,i had no previous w&t nor damage.
ticket was opened....
Seems Navy ships are stopping players for a checkup - read elsewhere you should see a comm chat about their intention...I got interdicted today in my python, I submitted right away but still received 35k worth of hull damage. What made this even worse was the fact that the npc that did this was a green friendly federal navy eagle that just turned and flew off without doing anything.