Minimap is showing all bottleneck entities as the train graphic on the minimap/map view (blue and red triangle). Also, the bottleneck r/y/g icons now cause collision and pathing in between two adjacent assemblers is not possible where the icon is in the path.

thats because they are vehicles, you can even get inside of them. they also get moved by transport belts, so yea, the mods broken for now.

I encountered the same problems. Especially the collision part and the "being moved by transport belts part" caused some "surprise" as after loading my game suddenly a whole lot of those indicators began moving around on conveyor belts.

To "fix" the current problem I downgraded to 0.5.2 which seemed to have worked.
I'm hoping there's a quick fix to this or at least a temporary rollback so the update mods function in factorio can be used again.

Chalking this up to a big oops. Rolling back to 0.5.2 will fix the issue for now. and I should be able to push a fix to trold shortly.

The weird thing is the icons have no collision box :(

Oops... I will have a look at it tonight.