To reproduce the issue:
1. Crete new project (or open any other project)
2. Add cylinder GameObject into the scene
3. Inspect the collider of the cylinder GameObject
4. Capsule collider is attached to the cylinder GameObject
5. Look the collider shape in the scene view

Expected: Collider should match geometry of the game object. Probably mesh collider could be used.

Screenshot:
http://screencast.com/t/OhRRHvtXx

Workaround: Changing capsule collider to the mesh collider

Reproduced in 5.4.0b5, 5.3.2p2, 5.2.2p4