The person who initially called police the night of the incident told ABC7 the teenage suspect had been acting unruly before officers handcuffed him.
Police have given almost no details about the incident to the media and to the officers' union, which says it's now considering legal action against Chicago Police Superintendent Jody Weis.
The alleged beating happened at 79th and Vincennes. But the police union said Wednesday a squad car's GPS shows two of the accused officers weren't even there.
"At least two officers, and potentially all seven department members, have had their careers damaged by the superintendent's lapse of sound judgment," said Mark Donahue, president, Fraternal Order of Police.
Witnesses say the alleged incident happened early last week in the parking lot of a fast food place. Shawn Aslam was working there that night when he said the teenage suspect entered and began making threats.
"That boy who got beat up, he comes here. We know him personally, but he never did it before. That night he was mad, he was just smashing the door and everything, but we just called the cops," Aslam said.
Aslam said he was working and did not see what is now being investigated.
A sergeant allegedly punched the handcuffed teen in the jaw while other officers watched, leading Supt. Weis to reassign the seven men to desk duty.
"If he insisted upon carrying out this investigation in the media, I would have first like to see him apologize to the two officers who've been cleared. Didn't happen," said Donohue.
In a statement, Chicago police said, "the department is committed to cooperating fully with all [Independent Police Review Authority] investigations. It is important to note that relief of powers does not constitute discipline."
The union called into question the investigation as a whole.
"I think common sense could dictate that there's a great potential that the allegations against the other five potentially hold the same amount of merit that the allegations held against these two officers," said Donohue.
Aslam said he did see the teenage suspect with a bruised lip later that same night. The union says neither of the two cleared officers is the sergeant who allegedly threw the punch. The union also says it found the GPS evidence, not police, and presented it to the Independant Police Review Authority.
Supt. Weis is scheduled to be a guest on ABC7's morning show which starts at 4:30 a.m.