Scott Rendell levelled in the 89th minute to make it 2-2 at Roots Hall, but the Chairboys returned to Buckinghamshire pointless after Craig Easton gave Southend a dramatic 3-2 win in injury time.
It was the second match in succession Waddock's side had let a draw escape them following their 1-0 defeat at Bradford on Saturday.
Waddock was left angry by their latest defeat, saying: "We have had one or two frustrating results this season and this ranks up there with them. I'm not pleased because we have not come away with anything. We have dropped a number of points over the last two games.
"I made changes for this game and I will make changes again for the weekend. We got ourselves right back into it and then conceded a third and shot ourselves in the foot.
"We warned the players before the game and at half time about letting sides back into the game and within a couple of minutes they have scored."
Source: PA
Source: PA