Filipe Morais scored the opener from the penalty spot in the 51st minute and Jordan Burrow netted the second to secure Stevenage a second round spot.
McCarthy "I thought the first half was all right, to be honest.
"We expected it to be a difficult game but we looked all right in the first half and then in the second half we give a penalty away that the lads are not too happy about, but until I see it I don't know.
"Then when I changed the team and put two lads on we had a bit of a resurgence but we gave another goal away that killed us off.
"I've no regrets whatsoever about the amount of changes that I made because I doubt I could play our two centre forwards, Daryl Murphy and David McGoldrick, in a game of that intensity week-in, week-out.
"The other two have to play and Dean Gerken has had not much to do apart from pick the ball out of the net twice so I've no regrets at all - they're all first-team players."
Stevenage manager Graham Westley said: "We're going to do a lot of learning this season and we're going to make a lot of mistakes and you can't do anything about that when you've got so many new players.
"They're having to learn a lot about each other so we're hoping that we can
win games while we're learning because there's some really good quality here.
"We lost very well at the weekend and tonight I thought we won very well and
we'll take the positives from tonight."