Sandbox has been created to protect servers and server owners from malicious plugins by limiting their functionality and access in the code, such as file API access, Harmony and more. You may recognize it by errors in your console like the following: UnauthorizedAccessException: System access is restricted, you are not allowed to use Harmony.HarmonyInstance.
In order to disable it, navigate to your server folder, go to /RustDedicated_Data/Managed/ and create an oxide.disable-sandbox file - it should not have any contents or any other extensions, this is the full file name. Restart the server afterwards and that is it!