Well everthing I see in your video seem to be just normal trains functions not glitched but a misunderstanding of how trainz works.
Its well none and documented thats Trainz does not handle safeworking at Dimond crossing its been with trainz form the very start there are ways around this is you looking into some creators rules.
As to not stopping at the end of the rails how about setting lower speed limits so trains go alot slower in yards, that and invisable stop signals at the end of the track helps.
As to the signalling you need to set up your signalling to suit trainz not how you think it should be done in real life, once again there has been many postings over the years that you should search out in the fourms and read.
As to cars runing through at crossings it has never worried me it called Trainz not Carz
As to trains derailments - remember its a game - and it needs to keep its G rating