I think it's because of issues like this that Autocad seems to encourage people to put all their labels in paperspace. They have valid reasons for this position, but I've found that modelspace labels are superior in some tasks. It depends on what you're doing.
If you put labels in modelspace, I've found you can minimize conflicts if you try to set up your drawings so that as few labels as possible are in XREFd drawings. If possible, try and keep all your base drawings "linework only". When you must have labels in a base drawing, try to put labels with different purposes on different layers, if possible. That way, in case of a conflict, you can always freeze just the offending layer in your main drawing, and it has less of an impact than if all the labels are on a single layer called "TEXT", or some such.