But the head coach vowed the Blues will finish in the League One play-offs over his 'dead body'.
Pompey suffered a 1-0 loss to the mid-table Dons on Saturday, which stretched their winless run to three matches.
Cowley was left concerned for the first time during his short tenure in the Fratton Park hot seat as the Blues lost ground in the League One promotion race.
And the ex-Huddersfield chief had to bite his tongue when addressing his players – and wouldn't disclose what he was thinking afterwards.
Cowley said: ‘There were a few bits where, for the first time, I didn't like.
‘I'm going to go away, reflect on them and look at the group going forward.
‘We've had seven games and taken 13 points. We always try to take an average of two points per game, that's what it's always been throughout our career bar a relegation at Huddersfield.
‘If you want to be a successful team, you need to average two points per game.
‘We are disappointed with this week. We've not got to the levels we want to achieve and the standards we set ourselves.
‘I saw some bits that I didn't like. I think that should always be kept between us and them but I haven't told them and haven't gone into detail yet.
‘I'm frustrated and disappointed so sometimes you have to self-regulate to be able to communicate effectively.’
Pompey's defeat at MK Dons means they've dropped to seventh and out of the play-offs – while eighth-place Charlton are two points behind with a game in hand.
With five matches remaining, the Blues' promotion hopes hang in the balance.
However, Cowley insisted he'll he do all in his power to ensure Pompey finish in the top six.
He added: ‘Like I said to the players, you have two choices in life. You either look out the mirror or out the window.
‘The people who look out the window tend not to be successful. The people who look in the mirror tend to look at what they can improve and tend to go on to have success in this world.
‘That is what my message is to the group. There'll be a lot of disappointed people associated with Pompey but we're going to come back in on Monday and show resilience.
‘I promise you this: over my dead body are we not getting in the play-offs.’