Ok after Much testing I got a video of the start of the issue. I rebuild all my trains on one loop and watch the bugs occur. Here is a video of the problem starting.
Looks like the switch system has a big bug. If you watch closely the switches change for the train behind the one in front way to early. This splits the train in front.
If you have only one train on a line this will not happen. If all trains stop at all station in a row does not seem to occur( need to test more). Fixed all my trains and stop all but one on that line for now.
Also problem seems to occur sometimes when a train blows through a station to when one train is loading. Have not been able to reproduce yet though.