The hosts at Fratton Park created a handful of clear-cut opportunities, but failed to capitalise – before the visitors raced into a two-goal lead before half-time.
Connor Ogilvie and Ronan Curtis perhaps squandered the best openings during the first 45 minutes.
The centre-back fired over from close range during the early exchanges and the Republic of Ireland international couldn’t make the most of his effort.
And Whittingham explained how the defeat was a missed opportunity by the hosts.
Speaking on BBC Radio Solent he said: ‘Well I think Portsmouth, for 65 minutes, were the best team. It’s what you do in those 65 minutes and the opportunities you give the opposition in the 25 minutes they have.
‘Overall, I think it was 50-50 in terms of the possession and Pompey had 22 shots to MK Dons’ 14, but six on target. When you have that many shots, you’ve got to score more than two goals if you want to win games.
‘It’s disappointing because it’s against a team that, if you’d won, you have two games in hand and are three points behind which gives the opportunity to catch up. MK Dons were thrilled at the end, they saw it out well and did what they needed to do.
‘Pompey created two chances as good as MK Dons’ in the first half with Ogilvie and Curtis, and did not take them. They then found themselves two-nil down.
‘It’s especially important to take those chances against teams who are in competition for where you want to be. Good performances have got to result in good wins for your side and at the least, not losing.’
The striker had been heavily linked with a move to Pompey in the past – but a deal never materialised before his move to Stadium MK.
And Whittingham explained how Danny Cowley’s team would benefit from having a striker with his ability in their ranks.
He continued: ‘Ultimately, they’re missing someone who can put the goal away like Eisa did. I said during commentary he doesn’t really get involved in the build up in the way MK Dons play, but comes alive when the ball is in the final third – as he did for the goal.
‘In the opening 20 minutes, Ogilvie missed a good chance which was an open goal. He had to just keep it down and it’s in the back-of-the-net but it fell to a defender rather than a striker, I suppose.’
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