From what I've seen of the situation... Xayma should be right.
I think this happens:
At the instant you (the evil person trying to crash the train by sealing the tunnel) see the train going in, whereas the train is actually in front of where you think it is.
Because:
The light coming from the train took time in getting to your 'eyes'. In that time, the train moves forward as usual in its 0.9c supper-fast-speediness.
Think of two cars travelling from the same spot. One labelled 'photon' ,the other the train.
Therefore, like light coming from alpha centauri, you see a picture on the train in the past.
(And not only that, the light coming from each part of the train you see started from a different point in time. But that's not part of the question. This is apparent length contraction.)
Hence, you seal the tunnel, thinking that your machiavellian plan has succeeded. You see nothing happen in the same instant as light has just started travelling from the tunnel.
What you see afterwards is the train moving out of the tunnel effortlessly. Then you see the tunnel being sealed.