The problem is with 2DPlatformer package from AssetStore (https://www.assetstore.unity3d.com/en/#!/content/11228)

Regression from 5.6.0f3 (also works correct in 5.5.3f1)

How we can reproduce it using the example you attached
1 Open attached project (or download from AssetStore) in 2017.1.0a6
2 Press Play and try to jump on the UFO object -> its Collider doesn't work
3 Select in Hierarchy backgrounds->env_PlatformUfo, go to Inspector and find Polygon Collider 2D component

Actual result: the Polygon Collider 2D is broken and shows warning message (please see attached image in comments)

Expected result: Polygon Collider 2D should work after upgrading project