The 45-year-old faced criticism after seemingly announcing that cast members Lea Michele (Rachel Berry), Cory Monteith (Finn Hudson) and Chris Colfer (Kurt Hummel) would leave at the end of the third season before telling the actors themselves.
Michele later claimed to have been aware of her imminent Glee exit, but Colfer stated that he had been surprised by the move and wouldn't have chosen to leave the Fox show of his own accord.
Speaking at the LA premiere of Glee: The 3D Concert Movie last night, Murphy stated that the mix-up was now "water under the bridge", but confessed that he had been "surprised" by some of the stars' reactions.
"I'm glad it seems to have all died down," he told E! Online. "I was shocked and a little freaked out by that, I have to be honest.
"I felt that we try so hard with the cast to include them and make them feel like they're on top of the news, so I was a little surprised when a few of them said they didn't know it was happening. But water under the bridge."
Murphy also elaborated on the "back to basics" theme attached to Glee's third season, explaining: "We're doing fewer songs, more story. Nobody's breaking up this year which is very exciting."
Glee executive producer Brad Falchuk claimed at last month's Comic-Con that Michele, Monteith and Colfer will continue to appear on the show after graduating.
Watch the trailer for Glee: The 3D Concert Movie below: