I bought an SE but the lightning cable that came with it cannot be used in the cube. I don’t understand why this is done?
How do I connect this SE cord if it’s incompatible with cube? Why is this different?
iPhone SE, iOS 14
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By "cube" are you referring to the actual power adapter? If so, the 2nd generation iPhone SE came with a Lightning-to-USB-C cable, and yes, this would not work with the older USB-A power adapters. You would need to get a newer USB-C adapter to work with it.
As to the "why" my only guess is Apple is moving forward as USB-C is surpassing USB-A over time and they want to be ahead of the game. For the official reason, you will have to ask Apple directly.