Mustoe, who made his first start for Latics at Swindon, and fellow youngster Callum McManaman were the only plus points on an otherwise dismal afternoon at the County Ground.
Paolo Di Canio's men fought back from a goal down to win the game and pull off the upset of the third round.
Left-back Mustoe, 20, told the Wigan Evening Post: "I enjoyed it, I was made up to get my first start, although obviously I wasn't too happy with the result.
"I only found out a few hours before the game that I'd be starting.
"I had a good idea that might the case with the way training had gone this week, so I was prepared for it.
"Hopefully I've done well enough to show the gaffer I'm worthy of being involved at this level."