There is the 0870 phone number issue. Essentially, because some of the charges for 0870 calls go to the organisation being called, use of this number means the PCN represents an unlawful demand for money, being more than the penalty charge.
In addition, an adjudication (2018) on a DART PCN which is under the same legislation as low emissions zones, ruled that a PCN issued under the Road User Charges Act, and its associated regulations can only request payment of the penalty charge, and not add the road user charge on to it. So far this has not been tested for any PCNs issued for non-payment of tolls for non-compliant vehicles using one of the zones.
When you paid the toll, did you specify the date of entry into the zone ?