The Sandgrounders slipped to their fourth consecutive defeat, conceding 16 goals in the process and scoring just once.
Ashley Chambers' second hat-trick of the season for Nuneaton gave them their first victory in five to leave Lewer with concerns over his frontline.
"I'm disappointed, we should be 2-0 up in the first ten minutes and we haven't made the keeper make a save," he said. "I don't know what to say about us in front of goal, we don't look like scoring.
"I think there's a lack of confidence from when you lose games. We've missed senior players and it shows out there that you do need experience to turn games around.
"The injuries do cause you concerns. We had a team spirit to die for and then you lose them, and then you're bringing people in. I think Southport had that last year with a lot of players coming in and going and we didn't want that. Unfortunately we've had to because of injuries.
"It's a big factor but you have to get on with it and move on."
For more coverage, reaction and some of the best moments from games going throughout the season, head to our social media channels on Twitter, Facebook and now Instagram.