Butler was sent off in the 34th minute after leading with his elbow on Matt Tootle in an aerial challenge which left the Magpies full-back needing treatment.
It proved a turning point in the game as Notts went on to bag three goals against the Exiles and could easily have got more, with Jorge Grant nearly sealing a hat-trick.
“The referee has got it wrong,” Flynn told the South Wales Argus. “It changed the game and it spoiled the game.
“I’ve been told by the fourth official that he [Butler] went in with excessive force.
“I don’t think the referee had control of the game to start with. I believe he’s made honest decisions but unfortunately he’s got a lot of key ones wrong.
“And, just to rub salt into the wounds, I’ve watched the third goal again as well and it wasn’t over the line. It’s not been a great day.”
Share your thoughts about this news story on Pride of Nottingham by signing up to the website, visiting the forum and joining in the chat with hundreds of fellow Notts County fans.
Fancy showcasing your brand or business on Pride of Nottingham? Click here to find out more about sponsorship and advertising opportunities with us.