McCarthy's side missed a play-off place by just two goals
Wolves beat Plymouth but agonisingly missed out on a play-off spot to Watford on goal difference.
Seyi George Olofinjana hit the winner in the 87th minute after he raced on to Freddy Eastwood's through ball and coolly chipped keeper Luke McCormick.
Michael Kightly had earlier missed from eight yards for the home side, while Andy Keogh failed to touch in a cross.
The misses proved crucial as a 3-0 win would have seen Wolves leapfrog Watford into the top six.
The hosts dominated early on and Kightly was the first player to miss a golden chance.
The winger was unmarked at the far post but slipped and sliced his shot wide after Keogh's shot deflected into his path off former Argyle striker Sylvan Ebanks-Blake.
Rory Fallon fired into the side-netting at the other end from a tight angle but it was Wolves who threatened next, Keogh's effort from Olofinjana's low cross slipping just past the far post.
The same combination almost paid dividends after the break when Olofinjana's cross was cleared against Keogh but it trickled just wide.
Plymouth replied with Jamie Mackie shooting wide when well-placed but still Wolves pressed forward and Keogh could not quite reach a cross-shot from Kightly.
Eastwood replaced Keogh with 25 minutes left but only had one chance which he pushed wide of the post.
The game was delayed by several minutes after a nasty-looking injury to Plymouth captain Krisztian Timar, who was stretchered off.
Olofinjana finally broke the deadlock and the teams played eight minutes of added time but Wolves could not find the two more goals they needed to overhaul Watford and snatch the final play-off spot.
It was a disappointing finish to the season for Wolves, who reached the play-off semi-finals last season.
However Plymouth will be pleased with their 10th-placed finish, one place above last season.
Wolves boss Mick McCarthy:
"If we'd nicked it 1-0 I guess we would not be feeling so bad, but we haven't, we've had loads of chances and not managed to score three goals.
"That one game has been a reflection on the 46 this season when we have been dominant and not scored.
"But the lads have worked their socks off and we have had 19 clean sheets."
Plymouth boss Paul Sturrock:
"Our goalkeeper can't think of a save that he's had to make.
"He's finished up with the one chance through the middle and other than that I don't think there's anything he has had to make an incredible save from."
On Timar's injury Sturrock added: "We don't know how serious it is, he has been rushed to hospital but it doesn't look good. It would be unprofessional for me to guess what it is so we will wait to see what the specialists come back with."
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