The case will move to a February 15 preliminary hearing.
Head coach Andre Montgomery, assistant coach Karl Williams and athletic director Allard Nayadley were in county juvenile court facing charges of failure to report child abuse and/or child sexual abuse in the county where the victims live.
Prosecutors say the three men did not adequately notify the proper authorities of the allegations.
Attorneys for the three men filed motions to dismiss the case because it happened in a different county and because the head coach did file a police report at the hospital where he took one of the victims.
Nayadley's attorney also argued that his client was in Gatlinburg with his family to watch his son play in the tournament, and that he was not there in his capacity as Ooltewah athletic director or assistant principal. Nayadley was not staying at the cabin where the alleged assaults took place, but 10 miles away with his wife and daughter, his attorney said.
Ooltewah is a suburb of Chattanooga about 130 miles southwest of Gatlinburg, but the assaults allegedly occurred in Sevier County while the team was traveling for a tournament.
Judge Robert Philyaw ruled that Nayadley is still a school administrator and refused to dismiss charges.
"Protecting children is of utmost importance. There are laws requiring reporting of suspected abuse," Philyaw said. "Where you have a position of care or trust over children, you better know what your obligations are and don't rely on that organization to tell you."
Defense attorneys have requested that evidence and witness testimony from the investigators in Gatlinburg be brought forth.
The Hamilton County District Attorney's office also said it is looking into "allegations of an ingrained culture of violence among the football and basketball teams at (Ooltewah High School) reaching back several years."
CNN has attempted to reach Nayadley, Montgomery and William for comment, to no avail.
The case began after one of the boys required emergency surgery for injuries he suffered during a December 22 incident at a cabin in Gatlinburg.
Three juveniles face aggravated rape and aggravated assault charges in connection with the incident.
Court documents obtained by CNN affiliate WTVC show that a 17-year-old teammate is being charged with sodomizing a 15-year-old with a pool stick while two 16-year-old teammates held him down; the victim's grandmother also told CNN about that detail. Gatlinburg police statements do not mention a pool stick.
The grandmother said there were no adults around when the incident occurred. (CNN is not naming her because identifying her could identify a sexual assault victim, which is against CNN policy.)
The coach rushed the victim to the hospital, police said. The boy was later sent to a hospital in Knoxville, where he underwent surgery. He has since been released from the hospital and is home recovering, his family said.
The accused teens will be in court on January 26 in Sevier County.
Montgomery has been moved to another position within the school system where he will not interact with students during the investigation.
"I don't want anyone to think he's being punished or penalized. ... If we find other reasons to address the coach, we will. I've also instructed him not to be on the campus of any of our schools until this investigation is over," Hamilton County Superintendent Rick Smith said before charges were filed.
Smith canceled the basketball season on January 6, an action he said was not a reflection on the coaching staff, but was necessary so investigators could do their job.
He said he regretted not publicly addressing the issue earlier.