The problem involves booking sleeper reservations for more than one person. If you are not booking a sleeper, or you're booking for one person only, then you should be OK. If you are booking a sleeper for more than one person, you could run into this pricing bug. However, there is a way to check to see if you are getting the correct fare.
First, start the booking, but for just one person. Select your train and your desired room type. Put the selection in your "cart."
The cart will show two costs: one for the "Adult" rail fare, and a second for the room. Note the price of the room.
Hit the back button at the bottom of the page, and then change the number of passengers to 2. Select the train and your desired room again. Put your selection in the cart.
Once again you will see two prices. If the room price in the cart for two passengers is the same as the room price for one passenger, then the price is correct. You can just go ahead and book on-line. If the room price for two is higher than it was for one, that is an error. You should then call and make the reservation by phone.
I also prefer making reservations on-line. Reservations made by phone do not show up either on-line or on the smart phone apps.