Let's face it a plane that can go fast enough that if it were just crossing the Pacific coast and heading for the east coast when it got a "land on the Pacific coast", order, would be over Kansas before it got turned around, can be hard to identify under even good conditions - the close the encounter, the harder the identification...
Very well could have been... hard to ID a fast moving spec, or even estimate altitude. The only thing that makes me think otherwise is just how rare SR71 flights likely were in the late 90s.