Being Helpful or simply Correct?

The other day, I spent some time getting a new operating system up on one of our Simics virtual platforms. The platform is stable, the hardware is shipping and it is being used with the very software I was setting up. However, as the operating system was booting, I got quite a lot of warnings from Simics about incorrect hardware settings. The operating system still worked, however, so why did we see all these warnings? Actually, when is it prudent to issue warnings to a user about suspicious uses of hardware? When building Simics models, we want them to be helpful and offer warnings as much as possible - especially for cases where some uses might be considered technically "correct" but are actually somewhat suspicious.