I was told that I can’t ride a train with the pass that I have but I don’t know why.

Even if you have a pass, such as the Japan Rail Pass, which allows you to ride any train within a designated area, there may be some trains that are not covered by the pass. Also, there may be some situations in which you will be unable to take your desired train for reasons of passenger congestion. Please read the terms of agreement on the pass, and ask at the station the reason why you are not being allowed to take your desired train.