The blue train being discussed in the following post in a different bug report is more than likely another example of the same issue:

Questionable AI behaviour I enjoy Minimetro a lot, but I feel that I observe questionable AI behaviours really from time to time. Today I wish to give to an example. Please have a look at the light blue and the green line that intersect at the "plus" station. Some seconds ago, the long light blue train left the "plus" station but did not take any rectangle-shaped passengers. Instead, the long green train takes all of them. This confuses me. From previous posts, I see the AI works with a cost approach. Isn't the cost …

Actually passengers not getting on the correct train and passengers getting on the incorrect train are two aspects of the same problem: your pathfinding algorithm is buggy.