One of the young filmmakers behind a controversial 9/11 conspiracy documentary was arrested this week on charges that he deserted the Army, even though he claims he received an honorable discharge.

Korey Rowe, 24, who served with the 101st Airborne in Afghanistan and Iraq, told FOXNews.com that he was honorably discharged from the military 18 months ago — which he said he explained to sheriffs when they pounded on his door late Monday night.

“When they came to my house, I showed them my paperwork,” Rowe said. “The cops said, 'You’re still in the system.'”

Rowe is one of the producers of "Loose Change," a cult hit on the Internet espousing the theory that the U.S. government and specifically the Bush administration orchestrated the Sept. 11 terrorist attacks.

The movie is set to be released in about 40 British theaters in late August, according to Rowe and fellow filmmakers Jason Bermas and Dylan Avery.

Police arrested Rowe at his house in Oneonta, N.Y., about 10:45 p.m. on Monday and took him to the Otsego County jail, where he spent a day-and-a-half before he was released, he said.

Rowe was turned over to officials at Fort Drum — the closest military base — who then booked him on a flight to Fort Campbell, Ky., where his unit is based, to try to straighten out why the military issued a warrant for his arrest.

“A warrant for my arrest came down and showed up on the sheriff’s desk,” Rowe said. “Where it came from and why it showed up all of a sudden is a mystery to me.”

A spokeswoman for the 101st Airborne said Rowe is in the system as an Army deserter.

“He was listed as a deserter in 2005,” said Lt. Col. Rumi Nielson-Green, public affairs officer for the 101st Airborne Division (Air Assault). “What we show is that he was absent without leave in June of 2005 and was dropped from the rolls in July 2005. … He has been apprehended for being a deserter.”

Rowe said he believes it’s an administrative error on the part of the military. Nielson-Green conceded that could be the case, but said it was all speculation at this point.

“Anything is possible,” she said. “If this is an administrative error, then that will come out in due process. … It may be as simple as that, or it may be more complicated than that. Errors sometimes happen.”

Rowe said he was sitting in his living room watching the show “Cops” and drinking a beer Monday night when police banged on the door.

“I thought it was the TV,” he said. “There was f-----g mad cops out there. I thought, here we go.”

There were at least five sheriffs on hand for his arrest, Rowe said. They told him he had an active-duty warrant from the military.

“They pulled a whole operation. They cut my phone lines. They came from the woods. It was crazy — it was ridiculous,” he said.

Otsego County Sheriff Richard Devlin said his understanding was that the arrest was much less dramatic and more routine than Rowe described, though he hadn't confirmed the details with the officers involved.

"Two deputies went to the house and arrested him," Devlin said. "There was no cutting of phone lines or anything like that. ... There’s nothing to indicate there were any issues. It was a standard arrest."

Rowe speculated that he might still be in the system because he didn’t update his address, and characterized the military’s record-keeping databases as ineffective and disorganized. He doesn’t, however, believe his work on “Loose Change” was a factor in his arrest.

“I don’t think there’s any nefarious purpose or political stunt, or that anybody’s trying to shut me up,” Rowe said. “At the same time, I can’t be sure about that.”

Asked whether Rowe’s arrest has anything to do with his involvement in “Loose Change,” Nielson-Green said “absolutely not.”

“We’ve never even heard of this guy,” she said, adding that she wasn’t aware of the movie until Rowe was arrested and reporters and bloggers picked up on the story.

“Loose Change” initially had a prominent American distributor behind it — Dallas Mavericks owner Mark Cuban of 2929 Productions — but he has since backed out, apparently because of nervousness surrounding the film's inflammatory claims.

Actor Charlie Sheen had signed on to narrate the theatrical version of the film, but he recently said he's taking a wait-and-see approach to whether he’ll remain a part of the project.

"Loose Change" makes the shocking claim that the World Trade Center's Twin Towers were brought down on Sept. 11, 2001, by the U.S. government in a controlled demolition. It also contends that the military flew a missile into the Pentagon.