With the new train conditions in .13, a train can stay at a stop for a LONG time, and having other trains decide they want to use that bit of track to get around another train, turn around, or whatever means they can get stuck behind a train at a station that won't leave for a long time. Not to mention when you're being safe by crossing the tracks "downstream" of the stop, only to be run down by a train blasting through at full speed...

You can design around the problem to some extent (waste space by adding a turn-around loop to the entry of every station, not build stations that "cut corners" on the main line, etc.), but the trains sometimes have a mind of their own.