Wolves boss Nuno Espirito Santo refused to clear up why Diogo Jota was left out after his side crashed out of the Carabao Cup.
Jacob Brown's first goal for Stoke earned the Championship side a 1-0 second-round win at Molineux.
Wolves' record buy Fabio Silva blew a wonderful chance for a debut goal when he shot wide from six yards with 15 minutes left.
Jota was a surprise omission having been an unused substitute for Monday's Premier League win at Sheffield United but Nuno did not offer the reason.
He said: "He wasn't available, these are decisions we have to make. We have to prepare the squad.
"It was a big turnaround, we have to take care of the players, improve our squad and our team and he was not available for the game. These are our decisions to make.
"He was not on the squad list. There was no confusion. When a player is not on the squad list sometimes they see the match, if they are away, they stay at home.
"It's because we have a bubble, we have to make a list, all those details. Nothing strange."
A forgettable game had few clear chances and while Wolves made the running for much of the match, resilient Stoke held firm.
They improved after the break and Steven Fletcher's shot was deflected over by Conor Coady.
Not even the introduction of Raul Jimenez could inspire Wolves and new £35million man Silva missed their best chance when he side-footed wide from six yards.
Nuno added of the 18-year-old Silva: "Him and Victor (Vitinha) are very young and have joined us just this season. It's about them knowing their team-mates better, us trying to create better movement, better solutions because they are talented boys.
"Fabio had a couple of good moments in the box, good movements and next time he will try to be more creative. We will try to work on that, those chances can be finished better."
The miss proved costly as John Ruddy let Brown's shot in at his near post three minutes from time.
Brown's strike was his first since arriving from Barnsley for £2million and Stoke's first this season to book a third-round home tie with Gillingham.
Boss Michael O'Neill said: "It was a great result for us against a very good team. You can come into these games and not have anything to lose and the boys handled the game very well.
"We made seven changes and everyone who came in did very well. It creates competition which is what we want.
"It gives us the opportunity to integrate some players and get some as fit as possible because we're going to go into a very demanding schedule. We're going to need the squad.
"When we looked at their team and they have a new £35million striker and Adama Traore playing up front I knew we were going to be challenged. They threw a lot at us but clean sheets give you a chance to win games."
