So I ran into this little nugget this morning while working on a C# WinForms project in VS 2008 (might be an issue in VS 2005 as well).
Compiler Error: The item "*.resources" was specified more than once in the "Resources" parameter. Duplicate items are not supported by the "Resources" parameter.
Seems that when I copied an existing form and renamed the copy to something else (using the properties window) the refractor tool decided that the source form name needed to be changed as well. Apparently this is a common issue as I did a search for the problem online. Normally when you do a rename in a code file you get the option to preview the changes and apply what you want to. If you do this in the properties window or rename a class file in the solution explorer it seems to just make the change without a preview and globally.
I think that I need more control with this feature so you can turn this off in the IDE under Tools (for VS2008):
Doing this still allows you to do your refactoring (via the context menu) but now you have more control over what gets renamed. And as an added bonus it's also a performace tweek to the IDE.