The free-flow Dart Charge replaced toll booths on the Kent side a year ago.
Figures showed that out of nearly 42 million chargeable journeys, UK drivers had about 1.5 million penalty notices and foreign drivers more than 340,000.
The AA said the system still had faults, but Highways England said there was still more work to do.
Edmund King, from the AA motoring organisation, said: "We still think it could be even better if they scrap the tolls altogether.
"You get some other drivers who hesitate around the crossing because they're a little unsure about how they pay, when they should pay, what hours apply, and even the signs aren't clear."
The Freedom of Information request submitted by the BBC showed that 41,367,973 chargeable journeys were recorded, 1,519,162 penalty charge notices were issued to UK drivers and 340,861 to overseas drivers.
Under the Dart Charge, the penalty fine is Â£70, which is reduced to Â£35 if paid within 14 days, but increased to Â£105 if a driver does not pay.
Dart Charge project director Nigel Gray said the scheme had successfully sped up journeys, with peak-time return trips now 15 minutes shorter, and hundreds of thousands of drivers had also benefitted from discounts of up to a third.
He said more work had to be done on improving traffic flow on the Kent side, but the Dart Charge was a medium-term solution to congestion at Dartford, while the long-term answer was a third Lower Thames Crossing.
He said: "Figures show that the vast majority of people are paying their Dart Charge on time and non-payment is being followed up appropriately.
"The first penalty issued for any vehicle includes an offer to pay any outstanding crossing charges within 14 days and have the penalty or penalties cancelled. This approach has been very successful and we have no plans to end it."
More than 1.8 million penalty charge notices have been issued to drivers failing to pay the new cashless payment system on the Dartford crossing.