At minimum it needs to pay attention to railroad crossing bars and bridges.
They show a 2D representation to the driver because that’s good enough for drivers, but I wouldn’t assume that represents how the system operates internally at every stage. Even navigating requires the concept of bridges crossing roads without intersecting them.
It is indeed known to have issues at railway crossings:
https://news.ycombinator.com/item?id=47783427
AFAIK, there's no issue with bridges that cross roads, however. It will just ignore a road that's above or below the one you're travelling on that doesn't intersect with yours. Just like a human driver would do.