Seems like this is right after transition to 1.16, which reset all trains, so just give trains time to spawn. Trains can only spawn at a station and where the station track is not reserved by trains behind. Given your number of trains, just get it going and wait, they will eventually all spawn. In the save you shared, there is only 14 trains remaining to spawn by 4:00, only 7 by 5:07, and only 1 by 6:00.

Your bigger issue you do need to fix is collisions. The game now tracks more accurately colliding trains, and you have three areas where they collide. 1) Cable car near cable car depot/museum - tracks are too close resulting in head-on collision and blocks both lines. Make a better right turn curve so it does not get into opposite direction track. 2) BART approach to East Bay Center - the signal is too close to junction and a train standing at this signal is in the path of the opposite direction train - move the signal away from the junction. 3) Warm Springs Plaza - same, signal too close to junction - move it further away.