I brought this up last week and nothing was resolved. It was thought that NGUI was updated improperly but after confirming it was indeed updated correctly, the issue still stood.
I'm coming back now with some findings:
It seems that if UI elements are deeply nested, there is something about it that breaks and causes them to become orphaned and require either restarting Unity or Force Deleting the objects. The bug only begins after entering Play mode, you'll see the UI elements 'stuck' and don't go away even after disabling them, and even after exiting Play mode.
Our only solution now is to just not nest UI elements so deeply.