The summer signing from Barcelona had never previously featured in the Premier League, but a knee injury to Robert Huth resulted in Hughes calling upon the 21-year-old.
However, Hughes has insisted that the Spaniard was one of his team's better performers.
"He did okay on a difficult afternoon and will be better for the experience. He wasn't the reason we lost. Out of the back four, he was one of the better performers," Hughes told The Sentinel.
"At some point we are going to have to learn about these players, and I feel Marc has been really patient. I couldn't keep disappointing him. I felt it was an opportunity to test him at this level."
Muniesa had made three Capital One Cup appearances for the Potters prior to his outing at Goodison Park.