The 19-year-old was dropped after twice turning up late in training sessions and the club put the news on their official website.
"Whoever decided to put this news out on the website is evidently confused," Raiola told Gazzetta dello Sport.
"I hope it wasn't (manager Antonio) Conte's own decision, otherwise it means he is unable to deal with these kinds of situations.
"Paul is very disappointed with what happened, both with his lateness, despite having a good reason for it, and not being a part of the squad.
"In the first instance, he only received notification of the training session time late at the night.
"The second time he had some appointments that the club itself had organised for him to go to."