The League Two side were knocked out of the FA Cup and Johnstone's Paint Trophy this week by Stevenage and Newport County respectively.
However, Whittingham has said that the players must not forget about the six-match unbeaten run that preceded the two defeats.
"Two defeats in a row can make you think that you're not doing as well as you should be. But we're four points off the playoff places and we've played a game less, so it isn't that bad," he told Portsmouth's official website.
"We've got 16 new players in the group and we always said it would take time, but we're doing okay. We told the lads not to think that there is anything drastically wrong – because there isn't.
"We have to remind ourselves of how well we've done in the league because we've been on a good run and looked tight at the back."
Portsmouth face AFC Wimbledon on Saturday.