This indeed seems to be a real issue. The error message mainly means that the data got from the registry cleaner engine does not match the data in the registry.
This can mean only two things:
1. Something is wrong in the registry cleaner engine.
2. The data has been changed in the registry between the time it was read by the engine, and the time the data was re-checked by the SafetyNetV2.
Most of the cases I have seen seems to suggest case 2, but it's still an annoying popup when it does occur. I will try to find a way to fix it for the next version, without giving away too much of the extra safety the system also provides.