I'm not 100% sure how it occurs, but when you login from a new device I think you are asked to provide a device name... It's been so long since I did it.... For me I wonder whether having two hubs may have something to do with it.. not sure.
In terms of how to deal with it and whether to remove one of them, that may be the way to do in the end, but before you do, I'd check the Is Used By section at the bottom of the device page for both devices. Check what apps or rules refer to the devices, making sure you adjust any references so they all point to 1 of the devices, then look at removing the other. If you want, I might try and look at this myself and report back anything I find.
I wouldn't expect the phone number to be captured in the device, that would be concerning if it recorded that I would think... The interaction with the phone is to send notifications via the app and to identify the device, I would not expect the phone number to be the method for identification on the HE platform.