What a council balls-up ! A bay and also double-yellow lines. The two are totally incompatible.
As you have paid all there is to pay, you should appeal this all the way to London Tribunals where I am pretty sure you'd win and get your money back, but first you must submit representations to Newham, who will reject them, of course. You then register an appeal at London Tribunals at no extra cost to yourself. I suspect the council may then back down, but there's no guarantee on this.