Robert Huth's second-half header from a Matthew Etherington free-kick gave the Potters the lead 10 minutes from time.
But Wolves had a golden opportunity to secure a replay when a last-minute penalty from Nenad Milijas was saved by Thomas Sorenson.
McCarthy said: "The missed penalty (by Milijas) does not make me unhappy with the performance.
"It is indicative of our performance because it is a missed opportunity.
"Ultimately we gave away a needless free-kick and got punished by Stoke who do it better than anyone else with free-kicks, corners and throw-ins. We dealt with it well most of the time - but not that occasion."
Source: PA
Source: PA