David Connolly's two goals put Pompey on course for the three points but Peter Murphy - who opened the scoring - rescued a point for Stanley.
"I am frustrated as we did enough to win more than one game," Whittingham said.
"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.
"I have two good strikers in Patrick Agyemang and David Connolly but have other players in their position so they are kept on their toes.
"Before the game I would have taken a draw but now I am disappointed."