The AP story is too convoluted and incomplete to determine what the truth of the matter was. In any case, someone lied. Regardless, I don't think the toll will be a factor on how this all washes out unless there was manipulation here to show that the sheriff needed 'reasonable suspicion' to stop the car in the first place. The question might be answered if it is known why the toll-taker waved to the sheriff to begin with. It was either to alert him that the this was the car they were looking for (regardless if he paid the toll or not), or she alerted him because the driver didn't pay the toll. They can't have it both ways, unless by rare coincidence the car the sheriff was looking for turned out to be the same one that didn't pay the toll. Maybe the video will help straighten it out.
I've never believed that they needed to fabricate a "blown toll" in order to stop the cars.
There was a watch out for them, an alert to the toll booth operators to watch for the cars, the booth operator saw one, flagged the sheriff who followed for several miles before pulling them over (in the mean time the 2 drivers admit to talking to each other on cell phones).
The concerned call from the woman at Shoney's should have been sufficient to stop the men for questioning (which they could refuse). The dog sniffing occurred outside of the car. When the dog hit on a scent, they had justification for a search.
The men were taken into custody and released.