As the ship decelerates to a stop, it will appear to be in multiple places at once. First the light from the stopped ship (and any time it was moving slower than light) will reach us. Then after that, the light from its FTL travel will catch up to us, so the ship will appear in two places at once. From there, the "ghost" of the ship would travel backwards as the farther light reaches us and the previous light fades.
In short, the effects would be very unmistakable, not to mention the blueshift we would see (though that could be caused by sub-light speeds too).
Edit: Granted, proving that this is FTL would be tricky. However, based on analysis of the event (let's say it was all recorded in good quality) we could say with probably 95% certainty that it was indeed FTL, especially if we then see the ship take off again.