A bolt is not going to make a train, or the ride un-safe, in fact it would probably take tens, or even more than that to make it remotely close to dangerous. I've seen a bolt issue before on Nessie, it was just one that held one of the car-back covers on and the ride ops took the bolt and put it back in on their own. The bolt you saw was probably for something minor as that, most-definitely everything crucial to rider safety had been checked multiple times. However, we'd have no way to know for sure.
Nessie is a very bolt heavy train, due to its older design. Most of them are used for aesthetics, and other very minor things. And the fact that it appeared on the station floor almost proves it would have to be something like I experienced up above, most of the crucial nuts and bolts are located on the under-carriage of the ride vehicle, which is far below the station floor.