Today I noticed some unexpected behavior when using the ‘Include Collections’ rule in Collection membership (this also applies to the Exclude Collections rule). When you select a collection that is the the only collection in a folder, it will also select the entire folder above. This also selects all of the collections in the above folder. It only happens the first time you select the collection, if you deselect and select again it behaves normally. As you can imagine, if you are not aware of this bug it could be very destructive.
Note: I have been able to reproduce this in SCCM 2012 R2 CU4 and 2012 R2 SP1.