This is by design at the moment. It would be difficult to change because if we require animations in folders to use a different name, it would break all existing projects which use animations in folders!
In the engine, animations are just a flat list, hence they have to have unique names regardless of their folder. The same goes for most things in Construct 2 actually: layouts, event sheets and objects must all use unique names regardless of their folder. The folders are just there to help you organise so you don't end up with one insane list of everything. I can't see a good way to change this easily right now, so I'm going to close as won't fix.