Gills left-back Joe Martin scored the only goal of the match in the 56th minute as the visitors stepped up their game in the second-half, something that Wycombe failed to do.
"I'm disappointed that we didn't perform well enough in the second-half to get anything from the game," said Waddock.
"Credit to them for their second-half, (Gills boss) Martin (Allen) has assembled a good squad of players. We matched them during the first-half, but in the second I was disappointed with the display
"It's especially disappointing to not be able to back up Saturday's win with another three points.
"We'll dust ourselves down and go again at the weekend. We'll be positive. In your first home game you want to give the fans something to shout about, but we'll bounce back."
