Hughton felt his Norwich side did not deserve to exit the competition, defended his decision to make six changes and bemoaned the missed chances which ultimately proved costly.
"A big shock," Hughton said. "You have to give Luton credit. They came here with a game plan, we found it very difficult to break them down.
"The good chances we did have we weren't able to put them away.
"We pushed and pushed and they caught us on a classic counter-attack. It was a poor goal for us to concede.
"We never expected an easy game today. We knew they would come motivated, organised, but you expect to break them down at some stage.
"I think they have been fortunate, but that's cup football. Ultimately we weren't good enough to beat them today."