This example shows how two different assets, put in two different assetbundles, are somehow treated as the same asset and the second one fails to load. So if you click on Red and then Blue, the blue material fails to load. If you refresh and then do Blue, then Red, the Red material fails.

These are two distinct assets, but somehow they're colliding.

Example project here: https://github.com/lpetre/unity_assetbundle_name_bug

And a hosted versions here:
http://u3d-assetbundle-name-bug.herokuapp.com/web/web.html
http://u3d-assetbundle-name-bug.herokuapp.com/flash/flash.html