To reproduce the issue follow the steps:
1) Open attached project
2) Select "Slenderman" fbx model
2) Add several clips to its animation list
3) Observe the index naming of the clips

Result: "Take 001" (default) the next clip will be named "Take 0010"
The expected result is: "Take 001", "Take 001 (1)", Take 001 (2)", etc.
... exactly the same behaviour as increments in the Hierarchy (duplicate GO).

Video Repro:
http://screencast.com/t/C79VhJCb

Reproduced in 5.4.0b5, 5.3.2p2, 5.2.2p4