This is expected use case and should work properly. It is likely a bug - I will investigate this. Thanks for the comprehensive repro case.
Edit: I've been attempting to reproduce this and I don't seem to be able to. Would it be possible to email a repro project where its at step 5? Should be able to catch it pretty easily then.
I get duplicated 2D Polygon Colliders on my main spaceship every time I hit 'play'. Without fail. As far as I know I'm not doing anything exotic. It's just a prefabbed tk2d sprite with an animator and 2 attach points (one of the attach points has a tk2d sprite in it). However, it also happens to the baddies, but far less often (they tend to be inactive in edit mode, tho).
As yet I cannot identify the difference between when the excess ones get added to the ship and baddies.