There are quite a few formations at the HS level where a covered receiver is intentional. Some offenses will overload for what will be a power run play. I know my son's team, which was triple option, would cover their TE on certain plays. They might even throw out of it but the TE would be staying into block but it was primarily a run.
Make note of it when looking at your formation but don't get excited about it and flag what turns out to be a running play.