Pretty much what the title says. While playing in career mode, I noticed my throttle during ascent was being adjusted as if the "Limit to terminal velocity" was enabled, even though the Utilities module was still locked and not visible on the menu.

I can also confirm that this happens. It seems when switching from saves, certain features of mech jeb can stay enabled, with no way to toggle them from the current save if they have not been unlocked.

Yes that's the case, I had to even tell it to close the windows for
modules not yet unlocked so that's a feature that was until now
forgotten to be also checked so it simply carries the last setting over.
I'll see that I get a fix for that thrown at him.

The setting was probably still set to active the lasttime you used it.
There was also a bug where windows stayed visible if activated even
though you didn't have the module.
So I guess that needs to be extended to disable a module's function if
it's not available, not only closing it's window.

Closing this as an old MechJeb issue. Many MechJeb issues have had little interest in years, have been fixed for years, do not include adequate replication steps, refer to old problems which are no longer applicable, or are difficult to determine what the problem is. This issue is being closed for one of those reasons. We apologize for any inconvenience, but keeping the TODO list tidy helps the developers.

If this bug/issue is still a problem, please open a new issue. For bugs please try to include a Minimal, Complete, Verifiable Example that explains all the steps required to replicate the issue. A link to the KSP.log file should be ideally included, but is often not sufficient information. Screenshots or short videos are often the best way to show a bug.