Sometimes when you do an upgrade to a device, an arbitrary "discount" is applied to the full cost of the handset on EE's system so it will link the device to the plan you have i believe, it does not mean you should have to pay anything.
It is likely a result of the "estimated bill" feature in the app getting confused before the bill has been generated with the equalising amount.
Any time you see a minus on a bill, this is usually a credit to your account, not something you would have to pay in any case.
Essentially EE put the 1300 credit (to your account) on your account and the 1300 "charge" of the device (from your account), and as such the two cancel each other out.
Strange way to present things, I know. But it shouldn't impact you in any way.
If you have any concerns, it would be worth getting in touch with the billing team on 150. Once the bill generates properly for the first time after your upgrade, it should equalise and just be the new monthly charge and any part charges due to the date you changed plan mid-month and the plan you changed from and to.
