You see this sometimes with incorrect start position and RO continuing with commands. It's ultimately the ROs fault because "Make Ready" should be re-issued if the competitor is in incorrect start position. Even though it's technically the ROs fault if the competitor is allowed to shoot the course they MUST re-shoot.
In this case, let's say the RO was thinking it was only supposed to be a procedural, so he allows the shooter to continue. At the end of the course he is told that it is not in fact a procedural but should have been a stop + re-shoot. Despite it being the ROs fault, you must still re-shoot. If you refuse to do so you will be marked DNF on that stage.