I'm gonna be honest with you guys. When I opened a route I was working on and saw a bunch of railroad crossing devices where other buildings were supposed to be, I thought I had finally lost it. I call my sister into the room and she confirmed that we were in fact looking at a bunch of railroad crossing devices that I didn't put there.
This glitched started off small. One train station building was replaced by a railroad crossing device. I found the station that was supposed to go there, used the "replace asset with selected" tool and placed the station back thinking, "that was weird..." One day later, pretty much every building is now a railroad crossing.
This glitch started after adding five ATLS crossings to the route, but the crossings that are replacing the buildings do not match any of the crossings I place down, and the buildings are all being replaced with the exact same crossing device.