I'm thinking this is one of those funny rules things that signaling won't help and the program doesn't cover (correctly). In my experience with Trainz, there are some serious holes in terms of the AI operating rules, as there seems to be an inability of the AI to operate in anything other than signaled territory.
In my experience (NORAC), yards or "yard limits" are authority by verbal permission and are sort of a no-mans-land where you have to watch out for everyone else, while signaled territory gives you authority based on the signal indication and you "own" that track. There are exceptions that occur, read the rulebook, it's that thick for a reason. My guess, not knowing the specifics of AI operation coding, is that the AI driver gets confused somewhere it the transition from signals to unsignaled yard, probably getting stuck in a decision loop and defaulting to "stop and ask for help" mode.
Yards Limits are generally under a "restricted speed" operating condition where you have to be under a certain speed AND slow enough to be able to stop short of something in your way. Being able to stop in "one half of range of vision" is the NORAC standard with a maximum of 20MPH (or 15MPH, read the rulebook). Yes, that means you are probably creeping along with that 10,000 ton train, and flying along light engine.
The AI drivers don't seem to communicate with each other like real crews, and are decidedly shortsighted in managing their routing in unsignaled areas. I haven't found any kind of "yard limit" signal/sign/track mark that enforces that condition in Trainz yet (and PLEASE tell me if there is one).