Chopper believes decision changed gameNeil Harris described Ben Thompson's 49th-minute sending in Tuesday's Professional Development League game against Crystal Palace as 'harsh'.
The Lions were trailing 1-0 to an early Fisayo Adarabioyo goal when midfielder Thompson was dismissed for a challenge on Sonny Black, leaving Chopper's side a man down for most of the second-half.
Despite putting up a brave challenge, a strong Palace side ran in further goals from experienced defender Paddy McCarthy and new signing Keshi Anderson.
"It was a harsh decision," said Lions U21s coach Chopper. "Usually at U21s level you would expect the referee to err on the side of caution and show leniency, and that was a moment for the ref to do it, but he made the decision and we had to get on with it.
"The red card did prove costly because, although we were a goal down at half-time, I was very confident of our ability to get back in the game. It was made that bit harder once we were down to 10 men.
"To be fair, we kept going, even at 3-0 with 10 men we kept pressing, harrying and the boys were an absolute credit, but they were just better than us. Realistically any chance we had of getting back in the game evaporated with that red card.
"We have a couple of poor goals away and it was disappointing; it's always disappointing losing to Palace but overall I have got no complaints."