Noticed this one on the weekend which is a really nasty one. If you link a source code file in two projects in your solution, the parser gets very confused until you reopen the solution. That i can live with.
However the serious problem is that if you perform a rename refactoring in the IDE on a method in that file then part way through the renaming it appears Resharper tries to open the other "link" of the file in the IDE and VS throws an error about the file already being open. Resharper doesn't roll back the refactoring and so you get left with a mess in your codebase as all the usages have not been updated but some code has been...