Yep, I suspect it has something to do with the "set of signals" the route uses. Right now I am using a purchased route (not N3V) with the BNSF signal set and it runs a 1 hour end-to-end session with no errors such as this. In my case clicking on the RED signal took me to a junction that simply blinked its red circle and arrows on and off. Sometimes remaking the junction helped but most of the time it did not. If you make a copy of the route and do a mass replace, in the copy, of the signals with latest Safetran or the BNSF set, that works in my case, you might have success. Note- I do have false REDS for almost a minute in the 2 places each time the session is run and one or two signals where there is only a brief false red stop. It is as if N3V is trying to create fake activity on the route in a poor attempt a simulating a working rail system with signals protecting you from "ghost trains".
N3v has made so many changes that we are now into unlucky customers that have some mysterious combinations of elements that offer them errors that few others have and where replication by N3V is difficult.