What you can deduce depends upon how many sensors you have, and whether you assume the acceleration of the train (not the speed) is zero or a constant value.
With only 2 sensors, (a start time trip, and a stop time trip), I don't think you have any way of determining the speed of the train going into the first trip. Hence, all you can do is say that the average speed between the trips is simply the distance between the trips divided by the time between trips. In essence, you're forced to assume (perhaps wrongly) that the acceleration is zero ... the train is at constant speed.
But that might not be the case. If the train is accelerating, you need some way to determine the speed of the train at the initial Point A. You could do this with two trips very close to each other (per the paragraph above), and then have a 3rd trip at point B further down the track. With this info, you now can use the standard equations of motion to determine the average acceleration between the points, and the speed of the train at Point B. See:
See the stuff under "Classic Version".
Hope this helps,