Jota was surprisingly left out of the Wolves squad when they lost to Stoke City in the Carabao Cup on Thursday after travelling with the team.
Speaking after that game, Nuno refused to give an exact reason for the forward's omission, saying: "Him and Max [Kilman] were not available for this game.
"We have a small squad, all of the options are good but today they were not available for the game. These are decisions that we have to make.
"We have to know what the moment of the season is. It was a quick turnaround but we have to take care of the players. We have decisions to make and we have to continue.
"When a player is not on the squad list, sometimes you see the match squad and stay away. We have to make a list but nothing strange."
Now, speaking ahead of Wolves' game against Manchester City on Monday, Nuno was more open, saying: "First I want to apologise to those on Thursday for my answers. But you understand.
"What Diogo did for us was absolutely fantastic. I think Diogo is going to the right place and we wish him all the best. He'll never be forgotten by our fans. Know we have to balance our squad better.
"We know the type of player want to bring and where we need to work on in our squad. Liverpool are going to have a great player and boy."
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The 46-year-old also confirmed that Liverpool youngster Ki-Jana Hoever would be joining Wolves, adding: "He will join us. He's a young player with talent and potential.
"This is what is happening. Diogo is joining Liverpool, and Ki will join us. He's not eligible for the match on Monday.
"Ki has a bright future ahead of him. We think this deal is good for everybody. Diogo was really happy here, but it's normal that players like to face new challenges."