But it was the way his side responded to Ethan Robson’s 72nd-minute winner which irked him more than anything else at the final whistle.
The downbeat Blues boss said he had words with his side at half-time about trusting the way he wanted them to play and being braver in their actions.
MK Dons had the better of the first half and were only denied the lead by some brilliant goalkeeping by Gavin Bazunu.
Denver Hume: Portsmouth's expensive forgotten man and why former Sunderland defender really could be one for the future
'Real driving force... lion-hearted display... classy presence' - Neil Allen's Portsmouth ratings from 3-0 Carabao Cup win at Cardiff
Cardiff 0 Portsmouth 3: Neil Allen's verdict - From Fratton boos to 'Just like watching Brazil' as brilliant Blues produce remarkable cup shock
Portsmouth transfer news: The four Fratton Park departures Blues could still sanction before window shuts - including ex-Sheffield United defender and Luton midfielder
'We’ve got a real problem': Portsmouth boss reveals headache after career first at Cardiff
Meanwhile, a Reeco Hackett-Fairchild header was all the visitors could really muster before the break – although the winger really should have scored with the chance presented to him.
The second half saw Pompey stamp their authority on the match, with substitute Ronan Curtis and John Marquis presented decent opportunities in front of goal.
The Blues were in the ascendancy but soon conceded on the counterattack – a blow which Cowley believes his side failed to recover from.
And it was that inability to respond which rankled with the head coach upon the conclusion of the game.
Speaking to The News, Cowley confessed: ‘I thought first half, we didn't commit to the way he wanted to play.
‘We spoke at half-time about being braver and trusting in the way we wanted to play, and we showed second half when we did that we were able to get the control of the game.
‘But to win football matches you need to play for 90 minutes and I think, if we are honest, we fought our way into the game, played well for a period in the second half, but then we conceded.
‘And the biggest disappointment in the whole game was the response after conceding.
‘It was disappointing because it happened at Wigan as well.
‘We’ve got to keep doing what we're doing but all of a sudden we're starting to give fouls away, starting to go too direct.
‘We’re not set up to go that way, so you have to keep committing to the way we play, we have to keep staying in the moment, not getting all emotional when things don’t go so well, when things happen in games like conceding a goal.
‘There was still 20-25 minutes left in the game, so there's definitely some learnings take from the game.’
The defeat to MK Dons is the Blues’ second in League One this season.
They currently sit 12th in the table – five points behind leaders Sunderland.