I have a 3D sceneView application that uses a work-around print function that creates a 2D map in the background from the same 'map' as the sceneView, and prints from that. This post explains the process: here. After switching to 4.6, having any feature layers or mapService layers turned to 'visible' in the sceneview, and thus the map view, causes the execute print task to fail. It doesn't throw any error in the console, just the error callback function. If I revert back to 4.5, with no changes in the code, it works perfectly.
Just wanted to throw this out there if anyone else has noticed issues around printing in 4.6.