I once asked What is the place to ask questions about Area 51? where Jeff Atwood reported that Meta Stack Overflow was the place for such questions. Clearly the question was asked before discussion.area51.stackexchange.com was created.
In What is the division of labor between MSO and the area51-meta tag on Area 51? Robert Cartaino says Meta Stack Overflow is not the place for asking about Area 51.
In a recent comment a developer said:
Area 51 bugs actually do belong here on Meta (yes, we realize this is a bit confusing). Area 51 Discussion is for talking about the proposals themselves, and not so much for pointing out bugs in the software.
Where should I report bugs I see only on Area 51?
I can imagine those bugs should be kept in a single place to avoid that who needs to check for those reports should check in two different places, but the FAQ for Meta Stack Overflow doesn't report any reference to Area 51.
The other problem I see is for those "bugs" for which there is really a setting in the user interface available to Stack Exchange staff; I don't see in which way a question would be interesting for any other users on Meta Stack Overflow who don't visit Area 51 at all. If that is the sign that general code is being used in a way that was not initially planned, or general code is not considering a specific case in which is called, that would probably be a reason to report the bug in the general meta.