I'm pretty sure it's all signaled correctly since I've used similar setups in the past and haven't had the issue. The train just flat ignores the red signal and runs right through like a maniac!

The wrecks seem to always happen at my main station; a train is offloading and another one approaches and occasionally runs through the red light, hitting the stationary train. I've replaced/repositioned the signals and even recreated the locomotives but the collisions just keep happening. Maybe something wrong with the layout somehow?
Arg.. Can't upload save. Blasted 3mb limit. Save files have gotten a lot bigger the last few versions huh?
Ok, here's the save. When you load it, just stand there and watch the signals to the left. After about 5 seconds, they'll all turn yellow and the train collision will occur.
http://www.filedropper.com/trainwreck
alternate: https://app.box.com/s/m2b02ae2o3h23dg7aru1