During one run I have gathered a couple of graphical problems on the Harlem Line I wanted to share. Trains clipping with platforms on balloon tracks have been mentioned already, but worth throwing that in. On approach to GCT at the beginning of the tunnel the most right line clips through the train - this definitely should have been caught in testing as it clips all the way into the cab. The freight AI trains while being very cool and welcome addition clip significantly with the Harlem River bridge. Some stations have 3D snow piles during winter improving the overall visuals - again great addition, but I guess they're made as an asset that is hidden underneath the route and brought up during the right conditions. This run was nearly 10am in mid-may with light clouds, so definitely no snow, but the piles were probably not low enough and poked through the map.
I have no illusion you can catch all problems a route has before releasing it to thousands of people... but these seem really basic. And I've not even mentioned the numerous trees going through the cab.