His Blackpool counterpart Gary Bowyer complained of being hit on the lip by a boiled sweet after his players and staff celebrated scoring their third goal in the fifth and final minute of injury time.
The Pool boss was left furious by the incident and demanded an immediate investigation from the FA.
When asked what he saw, Newport's caretaker boss said: "Tempers spilled over a little bit and I was just trying to calm the fans down.
"They scored the third, their manager got a bit excited, and so did our fans.
"I saw a young boy crying which I didn't like, so I was just trying to calm everyone down.
"I'm not sure if he was scared or upset that we'd lost the game."
After two successive wins, Flynn suffered his first defeat as Exiles boss but the former Newport and Blackpool player insists his men can still stay up.
He added: "I can't fault the boys' effort again. We gave away a poor first goal and I don't think it was a penalty.
"Their keeper made a great save at 2-1 that would have made it 2-2. We went for the equaliser and wanted to salvage something and they went and nicked the third."