Is it a ULEZ penalty, or a charge for going through the Blackwall/Silvertown Tunnels? They would be perfectly entitled to charge you for the tunnel toll if you hadn't paid it, given that the Dartford Crossing charges a toll as well. Outside of London the new Blackwall Tunnel (which used to be free) toll hasn't received much coverage, so most people in the country are probably still unaware of it.
To avoid the toll, you'd have needed to go off that diversion and through the Rotherhithe Tunnel (which in itself is an interesting experience!) or go over Tower Bridge to avoid the toll. Those wouldn't have been able to be on the official diversion route as they are unsuitable for HGVs.
As an aside though, I do think it's unfair that ANPR can be used to issue fines for toll bridges / tunnels with very little in the way of warning signs. They should be allowed to automatically charge, but there should be a nationwide system for registering your car to a payment card once and after that it only charges the toll rate not a fine.
When it was only the London congestion charge it was fairly well known, but unless I did research first, I'd not have a clue which out of the Tyne Tunnel, Mersey Tunnel, Humber Bridge etc charges and by which method.
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