And the Pompey boss made it clear those who came into the side in the absence of key men wasted their chance in Saturday’s dreadful 1-0 defeat at Whaddon Road.
Meanwhile, Cowley was aware of placing too much stress upon Clark Robertson after his injury issues this season.
Denver Hume was unavailable because of a back issue but is expected to return this week.
Cowley made five changes from the side who drew at Bolton, but felt with hindsight he should have played those he had reservations over fielding.
He said: ‘We had one or two injuries - Michael’s knee was a little stiff and Clark we had to be careful with.
‘Joe’s hamstring is tight so there’s various reasons.
‘We could have played them and should have played them, but ultimately if you do you’re running a risk with the games coming as they are.
‘So we felt it made sense to be intelligent.’
Cowley couldn’t contain his frustration and disappointment at what unfolded on Saturday, with angry supporters understandably making their feelings known on the full-time whistle.
The Pompey boss could understand that and made it clear - with Tyler Walker, Mahlon Romeo, Ryan Tunnicliffe, Shaun Williams and Ronan Curtis coming into the side - no one staked their claim for further inclusion.
Cowley added: ‘I would’ve expected the players who came in to step up and take the opportunity.
‘But ultimately they didn’t do that and we didn’t do that - but it’s always a “we” when we lose.’