The Portuguese winger was absent from the squad and allegedly left the ground before kick off during their Carabao Cup clash against Stoke.
Wolves lost the game, and Jota's situation at the club was on the minds of reporters afterwards.
"He was not available for the game," said the Wolves manager.
"We have a short squad and all the options are good, but him and Max Kilman were not available for this game.
"He wasn't available, these are decisions we have to make. We have to prepare the squad, have to know what is the moment of the season.
"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."
Asked about Jota staying to watch, Nuno said: "I was watching the game. He was not on the squad list.
"There was no confusion. When a player is not in 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."
On whether Jota would play in the upcoming game against Manchester City, the Wolves head coach finished: "I don't know. We have to see.
"You are going to speculate a lot. He was not on the squad list. Period."