Pompey had come from behind to lead in the closing stages before Peter Murphy equalised for Stanley, and Whittingham believes that his side did enough to "win more than one game" at the Crown Ground.
The 48-year-old told Sky Sports News: "I am frustrated as we did enough to win more than one game.
"I thought we looked a lot more solid than last week and shape-wise, we broke off well.
"I told us to keep at it at half-time as I know we will create chances and we did but unfortunately we conceded too."
Portsmouth's draw has left them in 21st position in the League Two table.